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PubMed1998

Expression, characterization, and detection of human uridine phosphorylase and identification of variant uridine phosphorolytic activity in selected human tumors.

Uridine phosphorylase (UPase) catalyzes the reversible phosphorolysis of uridine to uracil. We purified the enzyme from the murine colon 26 tumor using a two-step procedure through 5-amino-benzylacyclouridine affinity chromatography. Antibodies raised in rabbits against the purified protein revealed single bands in Western blots of normal human tissue and tumor extracts. The polyclonal antibody used to screen a human liver expression library allowed the isolation of a 1.2-kb clone that contained the entire open reading frame of the human UPase. The UPase cDNA has been expressed as a fusion protein in Escherichia coli using the pMal-C2 vector. The kinetic analysis demonstrated that the recombinant UPase preferentially uses uridine, 5-fluorouracil, and uracil as substrates, although lower levels of activity were observed with 2-deoxyuridine and thymidine. Clinical samples of human tumors and adjacent normal tissues were assayed for phosphorolytic activity and sensitivity to 5-benzylacyclouridine (BAU), a potent inhibitor of the enzyme presently in Phase I-II clinical trial. Activity in normal tissues appeared to be low but very sensitive to BAU (approximately 90% inhibition at 10 microM). Tumors had generally 2-3-fold greater activity compared with adjacent normal tissues. In breast cancer specimens and head-neck squamous carcinomas, however, uridine cleavage was only partially inhibited (40-60%) by 10 or 100 microM BAU. The BAU-insensitive activity requires phosphate and pH conditions similar to the normal enzyme, and the new phosphorolytic activity was independent from thymidine phosphorylase. The BAU-insensitive phosphorolytic activity in selected tumors, coupled with the potent inhibitory activity of BAU against the "classical" uridine phosphorylase in normal human tissues, provides the rationale for combining BAU with 5-fluorouracil in the treatment of breast and head-neck tumors.

Amino Acid Sequence↗

PubMedDate not supplied

Rapid identification of hemoglobin variants by electrospray ionization mass spectrometry.

The precise identification of human hemoglobin variants, over 700 human hemoglobin variants are known, is essential for prediction of their clinical and genetic significance. A systematic approach to their rapid identification is described. Traditionally this requires protein or DNA characterization which entails lengthy analytical procedures. To overcome these obstacles a rapid approach to variant hemoglobin identification has been developed using conventional phenotypic methods combined with electrospray ionization-mass spectrometry (ESI-MS). The latter requires only a small amount of whole blood (10 microl) but in most cases 2 microl would have been sufficient and no preanalytical steps, such as separation of red cells or globin chains, are necessary. Aged, hemolyzed blood samples can also be analyzed. This approach has been used to positively identify 95% of the variants in over 250 samples. The remaining 5% in which a variant was detected by phenotypic techniques were not resolved by mass spectrometry. Ninety-nine different abnormalities comprising 36 alpha-chain variants, 59 beta-chain variants (including 2 extensions), and 4 hybrid hemoglobins were identified. These include 15 novel variants. The application of ESI-MS described requires approximately 1 h to prepare and analyze each sample and has minimal reagent costs. The turnaround time on a single sample can be as little as 2 h. This technique can now be considered a useful additional tool for reference laboratories.

Amino Acid Substitution↗

PubMed1975

[Transferrin variants: significance and identification in paternity cases (author's transl)].

Transferrin phenotypes were determined in 3380 sera of unrelated persons of the western region of Germany with 97.60 percent for TfC and 2.40 percent for Tf variants. Identification was achieved by immunochemical means or through autoradiography. Relative mobilities in some variants were measured using Tf B2C (0.7) as reference. Application of Tf variants is demonstrated in paternity cases.

Clostridium perfringens↗

PubMed1989

Heterogeneity of chicken growth hormone (cGH). Identification of lipolytic and non-lipolytic variants.

The identification and biological activity of chicken growth hormone (cGH) charge variants is described. On the basis of electrophoresis and immunoreactivity chicken pituitary glands contain at least two "charge" variants (Rf = 0.22 and 0.3) which have different net charge but similar molecular weight (26,300 d). Both are immunoreactive but show different bioactivity with adipose explants, band 0.22 being lipolytic whereas band 0.3 appears to be inactive. The abundance of these cGH bands vary with age, both being higher in young birds and lower in adults. These results suggest that cGH variants may have different biological actions.

Aging↗

PubMed2000

Madelung's deformity. Surgical correction through the anterior approach.

A resurgence of interest in Madelung's deformity has developed recently because of improved operations for correction of the deformity, identification of the genetic loci for the condition in certain syndromal variants, identification of an anterior ligamentous structure tethering the carpus, and preventive treatments in growing children. The process is reviewed in this article and a new surgical technique is presented. The procedure is performed by way of an anterior incision that is more cosmetically appealing. The release of an anterior ligamentous structure described by Vickers is performed simultaneously with a dome shaped osteotomy of the radius. The fragments, once alignment is corrected, are stablized with temporary pin fixation and a long arm cast until the bone has healed.

Child↗

PubMed2001

Detection of avocado sunblotch viroid variants using fluorescent single-strand conformation polymorphism analysis.

A specific reverse transcription-polymerase chain reaction (RT-PCR) protocol has been developed for routine detection of avocado sunblotch viroid (ASBVd). Modifications in this diagnostic technique were made to enable fluorescent detection and variant identification using automated capillary electrophoresis (CE) and fluorescent single-strand conformation polymorphism (SSCP) analysis. Sixteen sequence variants characterized in a previous study were analyzed using CE-SSCP on two ABI 310 Genetic Analyzers. Significant differences were detected between data obtained from the two ABI 310 Genetic Analyzers indicating that an internal control must be run concurrently with the samples. The 16 variants could be classified into 11 groups based on the SSCP patterns. The statistical analysis of the migration rate data provided support for the visual differences in SSCP patterns. The use of SSCP in the ASBVd assay is easily accomplished and gives an estimate of the number of variants in crude samples extracted from infected avocado plants.

Base Sequence↗

PubMed2000

Differential expression of estrogen receptor beta splice variants in rat brain: identification and characterization of a novel variant missing exon 4.

Estrogen receptor beta (ER-beta) mRNA is found in abundance in rat brain. The distribution of ER-beta mRNA in brain differs from that of ER-alpha suggesting they subserve different functions. ER-beta mRNA has been reported to be variably spliced, in contrast to ER-alpha, resulting in numerous isoforms that possess different functional properties. The present study was undertaken to determine whether the isoforms of ER-beta mRNA are differentially distributed in different brain regions. In order to assess the range of transcript forms expressed in various brain regions in the same assay, a micropunch dissection technique was combined with semiquantitative RT-PCR. The relative abundance of each ER-beta isoform (beta1>beta2>beta1delta3>beta2delta3) was similar in all ER-beta positive brain regions with the exception of the hippocampus, which contained low levels of most isoforms and a fifth ER-beta isoform, which we are calling ER-beta1delta4. Based on its sequence, ER-beta1delta4 encodes an ER-beta that is missing exon 4. Initial characterization studies of this showed that it did not bind estrogen, and that, unlike ER-beta1, it localized to the cytoplasm when expressed in cultured cells. The distribution of ER-beta1delta4 was different from that of the other isoforms in that it was expressed at high levels in the hippocampus, where the other isoforms were low, and that it was nearly undetectable in the brain regions that expressed the highest levels of the other ER-beta splice variants. These data suggest that a highly complex pattern of estrogen signaling can occur in a region specific manner in the rat brain.

Alternative Splicing↗

PubMed1997

Cation-exchange HPLC evaluated for presumptive identification of hemoglobin variants.

A battery of relatively simple tests allows the presumptive identification of hemoglobin (Hb) variants, making unnecessary structural analysis by protein chemistry methods or DNA sequencing. The primary step in this strategy involves the use of a matrix of electrophoretic mobilities obtained under various experimental conditions. This leads to an unambiguous result in approximately 90% of the cases. Additional tests are required to characterize with more confidence the remaining 10%. We describe here the use of cation-exchange HPLC on the Bio-Rad Variant automated analyzer with the "beta Thalassemia Short" program. By comparing the elution time of 125 human Hb mutants, we found that some variants with almost identical pI values or produced by the same type of amino acid substitution displayed different elution times. We present several examples in which use of the HPLC profile helped establish the diagnosis.

Cations↗

PubMed1998

Diversity of naturally occurring Epstein-Barr virus revealed by nucleotide sequence polymorphism in hypervariable domains in the BamHI K and N subgenomic regions.

The extent of nucleotide sequence microheterogeneity varies among subgenomic regions of Epstein-Barr virus (EBV). We examined, in EBV-carrying lymphoid cell lines, the extent of polymorphism in EBV DNA fragments amplified from the BamHI E, K, N and Z regions, and then investigated the diversity of the more hypervariable regions in tissues and body fluids. In cell lines, sequence dissimilarities in a genotype-specifying fragment of the EBNA-3C gene varied from < 1-4% within each genotype; dissimilarities in the first intron of the BZLF- 1 gene were < 2% within each genotype. By contrast, dissimilarities in a C-terminal unique domain of the EBNA-1 gene, and in a fragment that encompasses and is upstream of the LMP-1 start codon, varied between 2 and 7% and were not genotype-specific. The sequence diversity in BamHI K and N regions was then examined in tissues and body fluids by single-strand conformation polymorphism (SSCP) analysis and cycle sequencing. Extensive inter-host diversity was observed, whether the host was co-infected by human immunodeficiency virus (HIV) or not. In the oral cavity of HIV-infected patients, inter-compartmental EBV diversity could be demonstrated, even between sites that were anatomically proximate. Studies of BamHI K clones derived from EBV in oral lesions revealed infection by multiple variants. Identification of hypermutable loci within the EBV genome such as those located in the BamHI K and N regions should permit fine discrimination of individual EBV variants.

Amino Acid Sequence↗

PubMed2024

ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.

The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.

Humans↗

PubMed1999

Capillary zone electrophoresis: an additional technique for the identification of hemoglobin variants.

Two capillary zone electrophoresis kits (Hb A2 and Hb A1c) were tested for confirmation and identification of hemoglobin variants. The capillary zone electrophoresis experiments were performed at pH 4.7 (Hb A1c kit) and 8.7 (Hb A2 kit) in a 24 cm uncoated fused silica capillary tube (25 microm I.D.). Normal hemoglobins and common hemoglobin variants, including Hbs S, D-Punjab, C, E, O-Arab, and G-Philadelphia, were successfully separated by both methods within a few minutes. Both systems provided completely different elution profiles of normal and abnormal hemoglobin fractions tested and were complementary. The inter-assay coefficient of variations of the migration times of hemoglobin variants were less than 1.0 and 1.3% by the Hb A2 and Hb A1c, respectively. This permits a higher resolution of some hemoglobin variants in low concentrations, like Hb S in newborns, compared with conventional electrophoresis methods. The present capillary zone electrophoresis methods are sensitive, rapid, not labor intensive, and highly selective for the separation of hemoglobin variants. Combination of both methods with some conventional methods, such as isoelectrofocusing, allows identification of Hbs C, E, O-Arab, S, and D-Punjab, as well as their quantification. We have demonstrated that the conventional electrophoresis methods (electrophoresis at pH 6.5 in citrate agar gel and electrophoresis at pH 8.6 on cellulose acetate) can be advantageously replaced by the present capillary zone electrophoresis methods in a clinical laboratory practice for the detection and quantification of hemoglobin variants.

Electrophoresis, Capillary↗

PubMed1994

A newly identified heterozygous lipoprotein lipase gene mutation (Cys239-->stop/TGC972-->TGA; LPLobama) in a patient with primary type IV hyperlipoproteinemia.

We investigated measures for identification of heterozygous lipoprotein lipase (LPL) deficiency in unrelated subjects with primary type IV hyperlipoproteinemia in order to acquire a helpful clue for understanding the correlation between hypertriglyceridemia and the status of being a heterozygous carrier of an LPL gene variant. Identification of heterozygous LPL deficiency was performed by monitoring the immunoreactive LPL mass in postheparin plasma (PHP) using our developed sandwich-enzyme immunoassay technique for first screening. Then, in subjects found to have half or less than half of the control LPL mass value in PHP, the polymerase chain reaction-single strand conformation polymorphism method was used to detect LPL gene aberrations as a second screening. This approach was evaluated as being useful as it succeeded in identifying a subject (proband KD) with heterozygous LPL deficiency. The mutation in the LPL gene of proband KD was newly characterized as a nucleotide C972 to A transversion in exon 6, resulting in substitution of a premature termination codon (TGA) for Cys239 (TGC). This nonsense mutation, designated as LPLobama, creates an MboI restriction site and eliminates an HgiAI restriction site, and this allows rapid screening of subjects with type IV as well as type I hyperlipoproteinemia for the mutation. The homozygous state for the LPLobama allele resulted in neither detectable LPL activity nor immunoreactive LPL mass in PHP, and this was seen in two of proband KD's siblings.

Adult↗

PubMed2025

Cycle threshold values and SARS-CoV-2 variant associations with breakthrough infections: a retrospective study in Accra, Ghana.

BACKGROUND: Breakthrough infections are defined as SARS-CoV-2 infections occurring ≥ 14 days after completing the primary COVID-19 vaccination series and remain a public health challenge, particularly in regions where immune-evasive variants are circulating. However, data on their virological and clinical profiles in low-resource settings are limited. METHODS: This retrospective study was conducted from July to December 2022 in Accra, Ghana, among individuals testing positive for SARS-CoV-2. Real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR) was performed using the Allplex™ 2019-nCoV Assay. Cycle threshold (Ct) values for the nucleocapsid (N), RNA-dependent RNA polymerase (RdRP), and envelope (E) genes, categorised as < 25, 25–30, or > 30. Variant identification targeted Alpha, Delta, and Omicron mutations using mutation-specific RT-PCR. Logistic regression was used to assess associations between vaccination status and demographic, clinical, and virological factors. RESULTS: Of the 268 samples analysed, 81 tested positive; 43.20% [n = 35] were vaccinated individuals. Median Ct-values for the N [27.13, IQR: 21.59–31.96] and E [24.57, IQR: 19.43–29.43] genes were significantly higher among vaccinated cases, indicating lower viral loads. Breakthrough infections were strongly associated with the Omicron variant [aOR = 4.38, p = 0.034]. Diarrhoea [aOR = 9.67, p = 0.022], sore throat [aOR = 8.99, p = 0.038], headache [aOR = 10.156, p = 0.039] and chills [aOR = 3.316, p = 0.046] were mostly associated with breakthrough infections. Ct-values of 25–30 [aOR = 11.33, p = 0.012] and > 30 [aOR = 4.01, p = 0.047] were significantly associated with breakthrough infection compared to Ct < 25 in breakthrough infections. CONCLUSION: Vaccinated individuals with SARS-CoV-2 infection had lower viral loads and were more likely to be infected with the Omicron variant. These findings reinforce the role of vaccination in reducing viral load and support the adoption of practical surveillance strategies, such as Ct value-based surveillance and variant screening in low middle-income countries facing similar constraints in genomic capacity and vaccine deployment.

Humans↗

PubMed2025

CAKL: Commutative algebra k-mer learning of genomics.

Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fundamental tool in algebraic geometry and number theory, has rarely been used in data and biological sciences. In this study, we introduce commutative algebra k-mer learning (CAKL) as the first-ever nonlinear algebraic framework for analyzing genomic sequences. CAKL bridges between commutative algebra, algebraic topology, combinatorics, and machine learning to establish a new mathematical paradigm for comparative genomic analysis. We evaluate its effectiveness on three tasks-genetic variant identification, phylogenetic tree analysis, and viral genome classification-typically requiring alignment-based, alignment-free, and machine-learning approaches, respectively. Across eleven datasets, CAKL outperforms five state-of-the-art sequence analysis methods, particularly in viral classification, and maintains stable predictive accuracy as dataset size increases, underscoring its scalability and robustness. This work ushers in a new era in commutative algebraic data analysis and learning.

Journal Article↗

PubMed1984

Isoelectric focusing in agarose gel for detection and identification of hemoglobin variants.

The use of isoelectric focusing in agarose gel was examined to test its usefulness for screening of cord blood hemoglobins and for the identification of hemoglobin variants in general. Advantages of agarose include: short running times, ease of preparation, and nontoxicity. In cord blood samples identification of Hb S, Hb C, and Hb Bart's was achieved. Separation of 16 hemoglobin variants, including six of clinical and geographical importance, was shown.

Electrophoresis, Agar Gel↗

PubMed1997

Identification of genetic variants of hepatitis A virus.

Although detection of hepatitis A virus (HAV) has been greatly aided by the development of polymerase chain reaction (PCR) technology, identification of genetic variants requires sequencing PCR products, which necessarily limits the length of the HAV genome (typically 2%) that can be analyzed. From a regulatory standpoint, identification of the specific strain detected by PCR is a prerequisite not only to overrule contamination of test samples in the diagnostic laboratory, but also to possibly locate the origin of the virus detected by PCR. We explored alternatives to sequencing PCR products to achieve these goals. The findings indicate that restriction fragment length polymorphism (RFLP) analysis of PCR products from two noncontiguous regions of the HAV genome encompassing 765 nucleotides (approximately 10% of the genome) by the restriction endonucleases HinfI and AluI, which cut frequently within the HAV genome, can distinguish the common tissue culture adapted strains of HAV from stool isolates. The resolution can be greatly enhanced by combining single strand conformation polymorphism (SSCP) analysis with restriction enzyme digestion, when most of the seventeen strains analyzed could be identified.

DNA, Viral↗

PubMed1994

[Identification of molecular variants of the enzyme glucose-6-phosphate dehydrogenase by the polymerase chain reaction technique].

BACKGROUND: An assessment of the usefulness of polymerase chain reaction (PCR) in the identification of the most frequent molecular variants of the glucose-6-phosphate dehydrogenase (G6PD) in Spain: G6PD A-, G6PD Mediterranean and G6PD Seattle through the screening of the mutations: 376 A-->G; 202 G-->A; 680 G-->T; 968 T-->C; 563 C-->T and 844 G-->C. METHODS: Three groups of patients have been studied: 1) males (40 cases); 2) relatives from the preceding group (31 cases: 7 males and 24 females), and 3) samples classified according to their fast electrophoretic mobility as G6PD A-(17 cases). The method used has been the PCR followed by digestion with specific restriction endonucleases. RESULTS: Group 1: 23 out of 40 samples (57%), were identified as G6PD Med563T variant (8 cases), G6PD A-376G/202A (13 cases) and G6PD Seattle844C (2 cases). Group 2: The study of relatives from 13 of the 23 identified samples allowed the study of additional 31 samples (7 males, 24 females): hemizygous G6PD Med563T (3 cases), heterozygous GdB/Gd Med563T (5 cases), hemizygous G6PD A-376G/202A (4 cases), heterozygous GdB/Gd A-376G/202A (11 cases), heterozygous GdB/Gd Seattle844C (1 case) and normal females (7 cases). Group 3: In all electrophoretically fast samples classified as G6PD A-was detected the 376 A-->G mutation (characteristic of G6PD A+). In 15 of these cases a second mutation was found at nucleotide 202 G-->A (G6PD A-376G/202A); and in two, at nucleotide 968 T-->C (G6PD A-376G/968C). CONCLUSIONS: The PCR method is fast and simple enough to allow the identification of known G6PD deficient variant, avoiding the need of its molecular characterization, which is more cumbersome and time consuming. In addition, the PCR is a very useful tool for demonstrating the carrier condition of G6PD deficiency in females with enzyme activity within normal range.

Base Sequence↗

PubMed1990

Enzyme immunoassay for the identification of hemoglobin variants.

We have prepared monospecific antibodies to Hbs D-Los Angeles, J-Baltimore, O-Arab and J-Paris-I and developed an enzyme immunoassay (ELISA) for their identification in hemolysates. Hbs in adult or cord blood hemolysates were coated to the wells of microtiter plates and reacted with the appropriate antisera followed by the detection system which contains anti-rabbit IgG/peroxidase conjugate and the substrate tetramethylbenzidine. Sixty-nine samples were tentatively considered to contain the above hemoglobin variants by isoelectrofocusing and the identity of 83% of them was confirmed by ELISA. Some of the non-reacting hemolysates were shown by amino acid sequence analysis to contain Hbs Korle-Bu, D-Ibadan, G-Copenhagen and the new variant Chandigarh. This ELISA offers specificity and simplicity for the confirmatory identification of hemoglobin variants.

Adult↗