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PubMed2006

Metabolite profiling and characterization of somaclonal variants in tea (Camellia spp.) for identifying productive and quality accession.

A study has been undertaken to characterize 15 field grown somaclonal variants derived from cotyledonary tissues of UPASI-10 using morphological, physiological and biochemical characters. Although variants were derived from UPASI-10, a very few variants possessed unique "Chinery" characters while others exhibited "Assam" characters. However, no variant showed identical morphological characters aligning with the parent. Somaclonal variants showed distinct variation in terms of photosynthetic carbon assimilation, stomatal conductance and diffusion resistance. Proline accumulation and water use efficiency showed marginal variations among the variants. SE 8 and SE 10 recorded higher values of membrane stability index denoting their tolerant nature against stress. Class interval analysis based on physiological parameters grouped these plants into three clusters. Three variants grouped under good category representing higher values of productivity index followed by five variants under moderate category. Green leaf constituents and quality profile of made tea produced with crop shoots of variants exhibited wide variation. Center point radar graph analysis of quality constituents grouped these plants into three clusters. Variants SE 2 and SE 13 were segregated distinctly representing their black tea characters. When considering both the quality and productivity indices, SE 3 and SE 7 fall under moderate category and in future these two variants may be subjected to further quality tests for commercial exploitation.

Amino Acids↗

PubMed2001

Collateral sensitivity to gemcitabine (2',2'-difluorodeoxycytidine) and cytosine arabinoside of daunorubicin- and VM-26-resistant variants of human small cell lung cancer cell lines.

Multidrug resistance (MDR), characterized by a cross-resistance to many natural toxin-related compounds, may be caused either by overexpression of a drug efflux pump such as P-glycoprotein, (P-gP), multidrug resistance proteins MRP1-3, or BCRP/MXR or, in the case of DNA topoisomerase II active drugs, by a decrease in the enzymatic activity of the target molecule termed altered topoisomerase MDR (at-MDR). However, human small cell lung carcinoma (SCLC) cell lines showed a collateral sensitivity to 2',2'-difluorodeoxycytidine (gemcitabine, dFdC) and 1-beta-D-arabinofuranosylcytosine (ara-C). H69/DAU, a daunorubicin (DAU)-resistant variant of H69 with a P-gP overexpression, and NYH/VM, a VM-26 (teniposide)-resistant variant of NYH with an at-MDR, were both 2-fold more sensitive to gemcitabine and 7- and 2-fold more sensitive to ara-C, respectively. MDR variants had a 4.3- and 2.0-fold increased activity of deoxycytidine kinase (dCK), respectively. dCK catalyzes the first rate-limiting activation step of both gemcitabine and ara-C. In addition, deoxycytidine deaminase, responsible for inactivation of dFdC and ara-C, was 9.0-fold lower in H69/DAU cells. The level of thymidine kinase 2, a mitochondrial enzyme that can also phosphorylate deoxycytidine and gemcitabine, was not significantly different between the variants. These differences most likely caused an increased accumulation of the active metabolites (dFdCTP, 2.1- and 1.6-fold in NYH/VM and H69/DAU cells, respectively) and of ara-CTP (1.3-fold in NYH/VM cells). Ara-CTP accumulation was not detectable in either H69 variant. The pools of all ribonucleoside and deoxyribonucleoside triphosphates were at least 3- to 4-fold higher in the NYH variants compared to the H69 variants; for dCTP and dGTP this difference was even larger. The higher ribonucleotide pools might explain the >10-fold higher accumulation of dFdCTP in NYH compared to H69 variants. Since dCTP is low, H69 cells might not need a high ara-CTP accumulation to inhibit DNA polymerase. This might be related to the lack of ara-CTP in H69 variants. In addition, the increased CTP, ATP, and UTP pools in the MDR variants might explain the increased ara-CTP and dFdCTP accumulation. In conclusion, the MDR variants of the human SCLC cell lines were collaterally sensitive due to an increased dCK activity, and consequently an increased ara-CTP and dFdCTP accumulation.

Adenosine Triphosphate↗

PubMed2003

Analytical evaluation of hemoglobin A(1c) dual kit assay on Bio-Rad Variant II: an automated HPLC hemoglobin analyzer for the management of diabetic patients.

OBJECTIVES: To evaluate the analytical performance of the Bio-Rad Variant II HbA(1c) dual kit assay. DESIGN AND METHODS: Precision, carryover, linearity and analytical range were investigated. 139 patients' HbA(1c) results analyzed by the Variant II were compared to the Variant I method. 49 blood samples analyzed by the Variant II at Toronto Medical Laboratories (TML) were compared to the Variant II at Hospital for Sick Children (HSC). RESULTS: Total imprecision was less than 2% for the Variant II assay. The method had a wide analytical range with no carryover. HbA(1c) results were not changed after switching back and forth from the beta thalassemia to HbA(1c) assay. The Variant II showed an average of 0.0027 negative bias compared to the Variant I method. There was an average of 0.0020 negative bias for HbA(1c) results on the Variant II at TML compared to the Variant II at HSC. CONCLUSIONS: HbA(1c) analysis on the Variant II HbA(1c) dual kit is a relatively fast and reproducible method.

Chromatography, High Pressure Liquid↗

PubMed1998

The genetic variant A of human alpha 1-acid glycoprotein limits the blood to brain transfer of drugs it binds.

The objective of this work was to check the effects of alpha-1 acid glycoprotein (AAG) and of its components, A and F1/S genetic variants, on the brain transfer of drugs they bind in plasma. The relevant extractions of six basic drugs, highly bound to AAG, were measured. We chose three drugs selectively bound to the A variant, disopyramide, imipramine and methadone, one drug mainly bound to the mixture F1/S, mifepristone, and two drugs which were simultaneously bound to the variant A and the mixture F1/S, propranolol and chlorpromazine. Their brain extraction were investigated in rats using the carotid injection technique and the capillary depletion method. Injected drugs were dissolved either in buffer, either in native AAG containing the three variants (A, F1 and S), either in variant A or in variant F1/S solutions. Brain extractions of disopyramide, imipramine and methadone were significantly reduced by native AAG and by variant A. Drug's plasma retention was related to their preferential and almost exclusive binding to A variant, both of them exhibiting the same decrease in brain transfer as compared to a buffered solution. At the opposite, there were no significative differences between the extraction either in buffer, either in AAG or in F1/S solutions, of drugs both bound to A variant and F1/S mixture (chlorpromazine and propranolol) or to the F1/S mixture (mifepristone). In serum, the retentional effect of the A variant on the extraction of disopyramide and imipramine was counteracted by the presence of albumin and lipoproteins, which simultaneously bind these two drugs at a high extent and act as permissive binders. We conclude that AAG binding decreases brain drug transfer when the A variant is mainly and almost exclusively involved in the binding. On the contrary, the entire fraction of the tested drugs when bound exclusively or partly to the mixture F1/S is available for transfer into the brain.

Animals↗

PubMed1999

Geographical distribution of variant CJD in the UK (excluding Northern Ireland).

BACKGROUND: The agent that causes variant Creutzfeldt-Jakob disease (variant CJD) is indistinguishable from the causative agent of bovine spongiform encephalopathy (BSE). The transmission route by which human beings are infected has not been established. One hypothesis is that cases of variant CJD have resulted from exposure to the BSE agent via rendering plants involved in the production of meat and bone meal, the main vehicle of the BSE epidemic. METHODS: We identified cases of variant CJD through the National CJD Surveillance Unit, and obtained lifetime residential histories of cases by interviewing a relative. The addresses of all rendering plants in the UK (excluding Northern Ireland) in production in 1988 were available from a survey done in that year. We calculated the distance between each case's place of residence on Jan 1, 1988, and the nearest rendering plant from postcode data, and used data from the 1991 UK census to estimate the population living within various distances of rendering plants. We compared the observed number of cases of variant CJD within a particular distance of a rendering plant with the number expected if there is no association between residential proximity to a rendering plant and the risk of developing variant CJD. FINDINGS: Up to Aug 31, 1998, 26 cases of variant CJD with onset in the UK (Northern Ireland not included) had been identified. The observed and expected numbers of variant CJD cases living within a specified distance of any rendering plant up to 50 km were almost the same. Two plants in the county of Kent each had four cases within 50 km in 1988, significantly more cases than expected (plant A, 1.04 expected; plant B, 0.74 expected). Multiple significance tests were done, so some tests would be expected to appear significant by chance alone. Computer simulations suggested that the observation of four cases of variant CJD living in an area with a population of 1.5 million (the size of Kent) is not unexpected. INTERPRETATION: There is no evidence that people with variant CJD tended to live closer than the population as a whole to rendering plants in the 1980s. The reported cluster of variant CJD cases in Kent is most probably a chance finding.

Abattoirs↗

PubMed1998

Structure and function of the ovine type 1 corticotropin releasing factor receptor (CRF1) and a carboxyl-terminal variant.

Corticotropin releasing factor (CRF) is the major neuropeptide regulating the hypothalamo-pituitary-adrenocortical axis in most species. A pituitary receptor for CRF (designated CRF1) belonging to the seven-transmembrane helix, G-protein-coupled receptor superfamily has been cloned for human, rat, mouse and xenopus. Since ovine CRF shares only 84% identity to human/rat CRF (h/rCRF) we postulated that the sheep pituitary CRF1 receptor may have similarly diverged from the rodent and human CRF1. We report the molecular cloning of an ovine pituitary cDNA containing a 1245 bp open reading frame encoding a 415 amino acid sheep CRF1 receptor 78, 86, 94, and 95% homologous to xenopus, chicken, rat, mouse, and human CRF1, respectively. The divergence in primary structure between the sheep CRF1 and the other mammalian CRF1s is primarily localized to the extracellular amino terminal domain of the receptor (18 of 22 divergent residues, ovine vs human CRF1). A variant of the oCRF1 was also isolated (oCRF1var) with 133 bp deleted from nucleotide (nt) 1080 to nt 1213 of the open reading frame (ORF) resulting in a new ORF of 1176 nt predicting a 392 residue CRF1 variant receptor. The 133 bp deletion would cause a frame-shift at residue 358 within the carboxyl-third of the seventh transmembrane domain (TM7) resulting in a shortened cytoplasmic tail with a new amino acid sequence from residue 358 to 392. Scatchard analysis of saturation curves using membrane prepared from Cos 7 cells transfected with oCRF1 or oCRF1var indicated that both wild-type and variant receptors were expressed similarly (number of CRF binding sites) and both bound oCRF with high affinity [oCRF1 (Kd): 2.5 + 1.6 nM; oCRF1var: 5.1 + 2.3 nM]. The non-hydrolyzable GTP analogue (GTPgammaS) lowered the affinity of both wild-type and variant oCRF1 receptors to a similar extent (oCRF1: 18.2 nM; oCRF1var: 22.4 nM). Both wild-type and variant oCRF1 receptors exhibited approximately 10-fold greater selectivity for oCRF and sauvagine compared to h/rCRF or alpha-helical [9-41]oCRF. CRF effectively stimulated the accumulation of cAMP (EC50 = 51 pM) in Cos 7 cells transiently transfected with wild-type but not variant oCRF1 receptor. In Cos 7 cells transfected with oCRF1var, cAMP accumulation was only observed at the highest concentration of oCRF utilized (100 nM). Basal (unstimulated) levels of cAMP in Cos 7 cells transfected with oCRF1var (in the presence of 2 mM IBMX) were approximately 50% lower than for the wild-type oCRF1. Differences in cAMP accumulation could not be attributed to differences in receptor number since total binding sites in the transfected cells were not different between wild-type or variant oCRF1 receptors. Agonist-induced receptor internalization, determined as the percent of total [125I] Tyr0-oCRF bound located in the acid-resistant fraction of transfected Cos 7 cells, increased with time (0-60 min at 37 degrees C) for both wild-type and variant oCRF1. Wild-type CRF1 internalized approximately 2-fold greater percent of total [125I] Tyr0-oCRF bound compared to the variant receptor. In summary, an ovine CRF1 and a CRF1 cytoplasmic tail receptor variant displaying high affinity binding to oCRF as well as selectivity for oCRF vs h/rCRF, were cloned from an adult sheep pituitary cDNA library. GTPgammaS studies indicate that both variant and wild-type receptors couple efficiently to Galphas however, only the wild-type oCRF1 is capable of stimulating cAMP production at physiological levels of CRF. Agonist-induced internalization of the ovine CRF1var is also reduced compared to the wild-type CRF1 receptor. We suggest that the oCRF1var interacts efficiently with Galphas but is unable (post-hormonal binding) to effectively stimulate G-protein activation of adenylate cyclase, indicating that the cytoplasmic tail of the CRF1 can modulate receptor function related to signal transduction. (ABSTRACT TRUNCATED)

Amino Acid Sequence↗

PubMed1996

Multiple splicing variants of the estrogen receptor are present in individual human breast tumors.

Transcript variants of the estrogen receptor (ER) were investigated in 109 primary breast tumors using reverse transcription-polymerase chain reaction (RT-PCR) and primers allowing analysis of each internal exon. A high incidence of different ER variants was observed, each individual tumor often manifesting multiple variants coexisting with corresponding wildtype (wt) ER. These variants, by sequence analysis confirmed to represent exon splicing deletions, included ER deltaE2 (found in 41% of the tumors examined), ER deltaE3 (74%), ER deltaE4 (72%), ER deltaE5 (66%), and ER deltaE7 (88%). No evidence of transcripts lacking exon 6 was found, although a ER deltaE5,7 variant manifesting simultaneous deletion of exons 5 and 7 was observed. The presence of specific ER variants was not significantly correlated to the status of ER and progesterone receptor (PgR) protein expression, as assessed by routine analysis, although a trend towards a higher incidence of ER deltaE3 and increased expression of ER deltaE7 in ER+/PgR- tumors was observed, suggesting a dominant inhibitory effect on normal ER function to be involved. Moreover, ER deltaE4 was more common in ER+ tumors, possibly due to a cytoplasmic sequestring of this variant lacking a nuclear localization sequence. The presence of ER variants was not associated to clinicopathological variables, and equally frequent in tumors from patients having recurred or remained recurrence-free during adjuvant tamoxifen therapy. In conclusion, although ER splicing variants are abundant in breast cancer, the present study provides no evidence for a direct role of these ER variants in tumor development and tamoxifen resistance. It remains possible, however, that minor cell clones within the tumor, undetected by analysis of tumor homogenates, displaying extreme difference in content of ER variants, could be selected for during therapy or metastasis.

Adult↗

PubMed1980

Antigenic variation in trypanosomes: a computer analysis of variant order.

African trypanosomes can undergo antigenic variation and evade the host immune response. Whether the antigenic variants arise in an ordered sequence or randomly has been in dispute but has not been statistically tested. The coefficient of concordance (W), a statistic designed to detect similarities between sequences of objects, was applied to the literature data. The tendency towards a reproducible order of variants was strong, although in several of the studies the number of experimental animals was so low that no conclusions could be drawn. A computer model was used to determine whether this degree of order could arise with random generation of variants followed by selection. The model simulated a trypanosome clone with 90 possible variants, widely differing variant-specific growth rates, random variant origin and variant eradication by an anamnestic host immune response. Parameters varied were maximum parasitaemia, growth rate differential between 'fast' and 'slow' variants, and parasitologist ability to detect minor variants. Random generation and selection by growth rate alone could not produce the degree of variant orderliness reported in the literature. However, experiments with larger numbers of host animals and direct investigation of variant growth rates and competitive interactions are necessary before the random generation-selection hypothesis can be proven or disproven.

Analysis of Variance↗

PubMed1995

Comparison of lethal and nonlethal transthyretin variants and their relationship to amyloid disease.

The role that transthyretin (TTR) mutations play in the amyloid disease familial amyloid polyneuropathy (FAP) has been probed by comparing the biophysical properties of several TTR variants as a function of pH. We have previously demonstrated that the partial acid denaturation of TTR is sufficient to effect amyloid fibril formation by self-assembly of a denaturation intermediate which appears to be monomeric. Earlier studies on the most pathogenic FAP variant known, Leu-55-Pro, revealed that this variant is much less stable toward acid denaturation than wild-type TTR, apparently explaining why this variant can form amyloid fibrils under mildly acidic conditions where wild-type TTR remains nonamyloidogenic. The hypothesis that FAP mutations destabilize the TTR tetramer in favor of a monomeric amyloidogenic intermediate under lysosomal (acidic) conditions is further supported by the data described here. We compare the acid stability and amyloidogenicity of the most prevalent FAP variant, Val-30-Met, along with the double mutant, Val-30-Met/Thr-119-Met, which serves to model the effects of these mutations in heterozygous patients where the mutations are in different subunits. In addition, we have characterized the Thr-119-Met TTR variant, which is a common nonpathogenic variant in the Portuguese population, to further investigate the role that this mutation plays in protecting individuals who also carry the Val-30-Met mutation against the classically severe FAP pathology. This biophysical study demonstrates that Val-30-Met TTR is significantly less stable toward acid denaturation and more amyloidogenic than wild-type TTR, which in turn is less stable and more amyloidogenic than Thr-119-Met TTR. Interestingly, the double mutant Val-30-Met/Thr-119-Met is very similar to wild-type TTR in terms of its stability toward acid denaturation and its amyloidogenicity. The data suggest that the Thr-119-Met mutation confers decreased amyloidogenicity by stabilizing tetrameric TTR toward acid denaturation. In addition, fluorescence studies monitoring the acid-mediated denaturation pathways of several TTR variants reveal that the majority exhibit a plateau in the relative fluorescence intensity over the amyloid-forming pH range, i.e., ca. pH 4.3-3.3. This intensity plateau suggests that the amyloidogenic intermediate(s) is (are) being observed over this pH range. The Thr-119-Met variant does not exhibit this plateau presumably because the amyloidogenic intermediate(s) do(es) not build up in concentration in this variant. The intermediate is undoubtedly forming in the Thr-119-Met variant, as it will form amyloid fibrils at high concentrations; however, the intermediate is only present at a low steady-state concentration which makes it difficult to detect.

Amino Acid Sequence↗

PubMed1985

A new variant of the anion transport protein in human erythrocytes.

The major plasma membrane protein of human erythrocytes is the anion transport protein, termed protein 3. We previously reported a variant form of protein 3 that is elongated on the amino-terminal end of the molecule, which is exposed on the cytoplasmic side of the membrane, but otherwise its features are identical with those of the normal molecule. We have termed this molecule protein 3 variant 1. We now report a new variant form, protein 3 variant 2. The erythrocyte donor was a double heterozygote whose red cells possess a normal protein 3 and a protein 3 variant which is elongated and possesses a second variation at the 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS) reactive site. Variant 2 reacts with 4,4'-diisothiocyano-1,2-diphenylethane-2,2'-disulfonic acid (H2DIDS) more readily than does the normal molecule. At high pH values, H2DIDS acts as a bifunctional cross-linking agent; it cross-links the proteolytic products generated by Pronase (or chymotrypsin) treatment of variant 2 less efficiently than noted for normal protein 3 or the first variant. Thus, the newly identified molecule has an alteration at the DIDS reactive site, which is near the outer surface of the membrane. The results can be interpreted as indicating that the DIDS binding site of variant 2 is more exposed than the normal molecule, but further removed from the site on the carboxyl-terminal fragment involved in cross-linking. Although there is a difference in the reactivity of the two protein 3 chains in variant 2, the reaction of variants 1 and 2 and normal cells with varying concentrations of [3H]H2DIDS results in the same amount of incorporation in all cells. Since protein 3 exists as a dimer or higher aggregate in the membrane, these results may indicate an interaction between monomers.(ABSTRACT TRUNCATED AT 250 WORDS)

4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid↗

PubMed2002

Kinetics of the biotransformation of maleylacetone and chlorofluoroacetic acid by polymorphic variants of human glutathione transferase zeta (hGSTZ1-1).

Glutathione transferase zeta (GSTZ1-1) catalyzes the cis-trans isomerization of maleylacetoacetate and the biotransformation of a range of alpha-haloacids. The objective of this study was to determine the kinetics of the biotransformation of maleylacetone (MA), an analogue of the natural substrate maleylacetoacetate, and chlorofluoroacetic acid (CFA) by polymorphic variants of recombinant hGSTZ1-1. The k(cat) of the four variants of hGSTZ1-1 with MA as the substrate followed the order: 1c-1c > 1b-1b > 1d-1d > 1a-1a whereas the k(cat) for the biotransformation of CFA followed the order: 1a-1a > 1b-1b approximately 1c-1c approximately 1d-1d. The turnover rates of MA were much higher than those of CFA for each variant and ranged from 22-fold (1a-1a) to 980-fold differences (1c-1c). The catalytic efficiencies of hGSTZ1-1 variants with MA as the substrate were much greater than those with CFA as the substrate, but little difference among the polymorphic variants was observed. MA was a mixed inhibitor of all variants with CFA as substrate: the mean competitive inhibition constant (K(ic)(MA)) for all variants was about 100 microM, and the mean uncompetitive inhibition constant (K(iu)(MA)) was about 201 microM. Hence, MA and alpha-haloacids apparently compete for the same active site on the enzyme. DCA-induced inactivation of the four variants showed that the inactivated enzymes show markedly reduced isomerase activities. The residual activities were different for each variant: 1a-1a (12%) > 1b-1b approximately 1c-1c approximately 1d-1d (<5%). This is the first kinetic analysis of polymorphic variants of hGSTZ1-1, and the similarity of the kinetic constants for hGSTZ1-1 variants with either MA or CFA as substrates indicates that few differences in DCA-induced perturbations of tyrosine metabolism would likely be observed in humans.

Acetates↗

PubMed2005

Novel variants in the putative peroxisome proliferator-activated receptor {gamma} promoter and relationships with obesity in men.

Yet unidentified variants within the peroxisome proliferator-activated receptor gamma (PPARgamma) 2 promoter may explain the inconsistent reports on associations between variants in the coding region and obesity or diabetes. Thus, we examined the putative PPARgamma2 promoter (-3371 to +43 bp) for variants in 83 subjects with obesity or type 2 diabetes. We identified eight variants, seven of which were novel, including -792A>G, -816C>T, -882T>C, -1505G>A, -1881C>T, -1884T>A, -2604T>C, and -2953A>G. The variants -816C>T, -1505G>A, -1881C>T, and -2604T>C were in total linkage disequilibrium, and there was a high degree of linkage disequilibrium between several of the novel variants and Pro12Ala. The novel variants were, together with Pro12Ala and 1431C>T, examined for relationships with obesity among 234 men with early-onset obesity with a BMI at age approximately 20 years of 33.2+/-2.5 kg/m2 and 323 nonobese men with a BMI of 21.7+/-2.5 kg/m2, who were also reexamined after approximately 29 years. The prevalence of the identified variants was not significantly different between the two groups, and the variants did not affect changes in BMI over time. In conclusion, the identified novel variants in the PPARgamma2 promoter region do not explain the reported discrepancies in the association of previously identified variants with obesity and type 2 diabetes.

Body Mass Index↗

PubMed2024

Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes.

Type 2 diabetes (T2D) genome-wide association studies (GWASs) often overlook rare variants as a result of previous imputation panels' limitations and scarce whole-genome sequencing (WGS) data. We used TOPMed imputation and WGS to conduct the largest T2D GWAS meta-analysis involving 51,256 cases of T2D and 370,487 controls, targeting variants with a minor allele frequency as low as 5 × 10-5. We identified 12 new variants, including a rare African/African American-enriched enhancer variant near the LEP gene (rs147287548), associated with fourfold increased T2D risk. We also identified a rare missense variant in HNF4A (p.Arg114Trp), associated with eightfold increased T2D risk, previously reported in maturity-onset diabetes of the young with reduced penetrance, but observed here in a T2D GWAS. We further leveraged these data to analyze 1,634 ClinVar variants in 22 genes related to monogenic diabetes, identifying two additional rare variants in HNF1A and GCK associated with fivefold and eightfold increased T2D risk, respectively, the effects of which were modified by the individual's polygenic risk score. For 21% of the variants with conflicting interpretations or uncertain significance in ClinVar, we provided support of being benign based on their lack of association with T2D. Our work provides a framework for using rare variant GWASs to identify large-effect variants and assess variant pathogenicity in monogenic diabetes genes.

Diabetes Mellitus, Type 2↗

PubMed2001

Myeloma isotype-switch variants in the murine 5T myeloma model: evidence that myeloma IgM and IgA expressing subclones can originate from the IgG expressing tumour.

Isotype-switch variants can easily be detected in a significant proportion of multiple myeloma (MM) patients. The biological significance of these isotype-switch variants remains obscure. Therefore, we studied the appearance of these isotype-switch variants in two murine MM models, 5T2MM and 5T33MM, both of IgG isotype. With a MM-specific PCR assay we could detect isotype-switch variants in the bone marrow of both the 5T2MM and the 5T33MM bearing mice, reflecting again the close resemblance of this mouse model to the human MM. These isotype-switch variants were not found in an in vitro stroma-independent variant of the 5T33MM line. However, when this 5T33MMvitro line was injected into young syngeneic mice, isotype-switch variants appeared thereafter in the isolated tumour cells. These isotype-switch variants could only originate from the MM-IgG expressing cell since IgG subclones from the 5T33MMvitro line again gave rise to isotype-switch variants. The appearance of IgA cells can be explained by down-stream switching of IgG to IgA, while the emergence of IgM cells have to occur via trans-switching to the sister chromatid as the Cmu region is deleted from the CIS-chromosome. This study demonstrates that isotype-switch variants originate from the major tumour clone suggesting no role for the MM-IgM expressing cell as a pre-switch precursor MM cell. The appearance of isotype-switch variants should be considered as a rare but normal event now becoming visible due to the high number of clonal cells present in MM.

Amino Acid Sequence↗

PubMed2004

Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment.

Several databases have been published to predict alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of expressed sequence tags (ESTs) to the genome sequence; however, little effort has been made to investigate the relationship between cancers and alternative splicing. We developed a program, Alternative Splicing Assembler (ASA), to look for splicing variants of human gene transcripts by genome-wide ESTs alignment. Using ASA, we constructed the biosino alternative splicing database (BASD), which predicted splicing variants for reference sequences from the reference sequence database (RefSeq) and presented them in both graph and text formats. EST clusters that differ from the reference sequences in at least one splicing site were counted as splicing variants. Of 4322 genes screened, 3490 (81%) were observed with at least one alternative splicing variants. To discover the variants associated with cancers, tissue sources of EST sequences were extracted from the UniLib database and ESTs from the same tissue type were counted. These were regarded as the indicators for gene expression level. Using Fisher's exact test, alternative splicing variants, of which EST counts were significantly different between cancer tissues and their counterpart normal tissues, were identified. It was predicted that 2149 variants, or 383 variants after Bonferroni correction, of 26 812 variants were likely tumor-associated. By reverse transcription-PCR, 11 of 13 novel alternative splicing variants and eight of nine variants' tissue specificity were confirmed in hepatocellular carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed.

Alternative Splicing↗

PubMed1968

Purification and properties of molecular-weight variants of human placental alkaline phosphatase.

1. Alkaline phosphatase of human placenta was purified by a procedure involving homogenization with tris buffer, pH8.6, extraction with butanol, ammonium sulphate fractionation, exposure to heat, ethanol fractionation, gel filtration, triethylaminoethylcellulose anion-exchange chromatography, continuous curtain electrophoresis on paper and equilibrium dialysis. Methods for both laboratory-scale and large-scale preparation were devised. 2. Two major molecular-weight variants designated A and B were separated by molecular sieving with Sephadex G-200 and variant A was purified 4000-fold. 3. Variant B, which comes off the Sephadex G-200 column before variant A, is the electrophoretically slower-moving species on starch gel and is quite heterogeneous. 4. Purified variant A was fairly homogeneous on the basis of electrophoretic studies on starch gel and Sephadex gel, ultracentrifugation and immunodiffusion. 5. The respective molecular weights for variants A and B were 70000 and over 200000 on the basis of sucrose-density-gradient ultracentrifugation. Variant A exhibited a sedimentation coefficient of 4.2s. 6. Crystalline variant B could be converted into fast-moving variant A and vice versa. 7. Kinetic studies indicated no difference between the two variants. These include linear rates of hydrolysis, pH optimum, Michaelis constants and uncompetitive stereospecific l-phenylalanine inhibition. 8. The amino acid compositions of variants A and B and of placental albumin were determined.

Albumins↗

PubMed1999

In vivo kinetics of human apolipoprotein A-I variants in rabbits.

BACKGROUND: Genetic variants of human apolipoprotein (apo) A-I, the major protein component of high-density lipoprotein (HDL), with a single amino acid substitution have been reported, and some of these result in very low plasma HDL-cholesterol (C) levels. Examining the kinetics of radiolabelled apolipoprotein is a straightforward technique for determining its metabolism in vivo. In this study, we investigated the in vivo kinetics of several human apo A-I variants, which we had identified previously, in rabbits. MATERIALS AND METHODS: Apo A-I variants from heterozygous carriers of Lys-107-->0, Lys-107-->Met, Pro-3-->Arg, Pro-4-->Arg, Pro-165-->Arg and Glu-198-->Lys and the corresponding normal apo A-I were purified and then radioiodinated with 131I and 125I. A kinetic study of apo A-I variants was performed in normolipidaemic rabbits after simultaneous injection of the two isotopes that had been incorporated into HDL. The fractional catabolic rate (FCR) was calculated from the radioactive decay curve. RESULTS: Acidic mature (negatively charged) apo A-I variants caused by a single amino acid substitution (Lys-107-->0, and Lys-107-->Met) were catabolized faster (FCR, 1.931 +/- 0.539 per day vs. 1.636 +/- 0.460 per day, P </= 0.01 using the Wilcoxon signed-rank test) and basic mature (positively charged) apo A-I variants (Pro-3-->Arg, Pro-4-->Arg, Pro-165-->Arg and Glu-198-->Lys) were catabolized more slowly (FCR 1.470 +/- 0.380 per day vs. 1.654 +/- 0.430 per day, P </= 0.01) than the corresponding normal mature apo A-I in vivo in rabbits. In addition, an inverse linear relationship was observed between the deviation in the FCR of variant human apo A-I from that of normal human apo A-I and the number of electric charges that the apo A-I variant carried (r = -0. 90, k = -0.188, P = 0.0003), as assessed by a linear regression analysis, suggesting that the electric charge of apo A-I variants may determine, at least in part, its in vivo kinetics in rabbits. CONCLUSIONS: Genetic variants of apo A-I with a single amino acid substitution show abnormal kinetics, and the electric charge of a apo A-I variant could contribute to determining its kinetics in vivo in this xenologous model.

Animals↗

PubMed2001

Association studies of variants in promoter and coding regions of beta-cell ATP-sensitive K-channel genes SUR1 and Kir6.2 with Type 2 diabetes mellitus (UKPDS 53).

AIMS: The beta-cell ATP-sensitive potassium channel consists of two subunits, SUR1 and Kir6.2. Population association studies have shown that three variants in SUR1 and one in Kir6.2 are associated with Type 2 diabetes. These polymorphisms do not result in a functional change or affect splicing, suggesting that they could be in linkage disequilibrium with a pathogenic mutation. The present study aimed firstly to screen the promoter regions of SUR1 and Kir6.2 to determine whether mutations in linkage disequilibrium with the silent variants lie in regulatory regions, which might lead to changes in gene expression. Secondly, novel and previously described variants associated with Type 2 diabetes (SUR1 exon 16-3t, exon 18 T, and Kir6.2 E23K) were investigated in the UKPDS cohort. METHODS: The promoter sequences of both genes were screened by single-stranded conformational polymorphism analysis for variants associated with Type 2 diabetes. The previously reported variants were evaluated in 364 Type 2 diabetic and 328 normoglycaemic control subjects. RESULTS: Two variants were detected in the SUR1 promoter, a three base insertion (caa) at -522 bp and a single base substitution at - 679 bp (c-->g). Neither of the variants were associated with diabetes, nor were they in a sequence consensus region for transcription factors. No association with diabetes was observed for either SUR1 variant. However, in contrast, analysis of the Kir6.2 E23K variant showed that the KK homozygosity was more frequent in Type 2 diabetic than control subjects. Variants were not associated with clinical characteristics nor did they affect response to sulphonylurea therapy CONCLUSION: There is no support at present for mutations in either Kir6.2 or SUR1 promoter sequences contributing to Type 2 diabetes. However, the minimal promoter region of SUR1 has yet to be investigated. The E23K variant of Kir6.2 is associated with Type 2 diabetes mellitus in the UKPDS cohort.

ATP-Binding Cassette Transporters↗