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At least 91 records · Page 5Linked to original sources
PubMed2000

Variant detection at the delta opioid receptor (OPRD1) locus and population genetics of a novel variant affecting protein sequence.

The three opioid receptor genes, and in particular the mu and delta loci (OPRM1 and OPRD1, respectively), are compelling candidates to influence risk for substance dependence. Previous study of a variant at the OPRD1 locus, T921C, has shown association with opioid dependence. This variant does not alter protein sequence, and could not be directly responsible for a physiologic effect. We sequenced the OPRD1 coding region in six individuals with differing T921C alleles, to identify new common variants more likely to explain the association with phenotype. We identified one novel variant in exon 1, 80T-->G, which predicts a change in amino acid sequence from phenylalanine (80T) to cysteine (80G) (F27C). We present here basic population genetics of this variant, and population genetic data for the T921C variant. We found significant differences in allele frequency between populations, and a maximum frequency of the 80G allele of 9%, in each of two European populations. This variant could contribute to the previously reported association results.

Alleles↗
PubMed1996

Intestinal fatty acid-binding protein: the structure and stability of a helix-less variant.

The structure of Escherichia coli-derived rat intestinal fatty acid-binding protein (I-FABP) exhibits a beta-clam topology comprised of two five-stranded antiparallel beta-sheets surrounding a large solvent-filled cavity into which the ligand binds. It also contains two alpha-helices that span residues E15-A32 and join beta-strands A and B. This helical domain is conserved in all proteins of this family for which structures have been determined. In order to assess the structural and functional role of the helical domain, we engineered a variant of I-FABP by deleting residues 15-31 and inserting a Ser-Gly linker after residue 14. Circular dichroism measurements indicated that this I-FABP variant, termed delta 17-SG, has a high beta-sheet content similar to that of the wild-type protein. Two-dimensional NMR spectra of delta 17-SG revealed patterns similar to those observed for wild-type I-FABP, except for the selective absence of resonances and through-space interactions assigned to the helical domain. The delta 17-SG variant was less stable to denaturant than wild-type I-FABP, but the folding-unfolding transition was highly cooperative and reversible. Taking into account the lower stability, the refolding kinetics of delta 17-SG were essentially identical to those of wild-type. We conclude that delta 17-SG is a helix-less, essentially all-beta-sheet variant of I-FABP and that the helical domain is not a required element of the beta-clam topology of I-FABP. In addition, the helical domain does not appear to serve as a nucleation site for the refolding process. As shown in the accompanying paper [Cistola, D. P., Kim, K., Rogl, H., & Frieden, C. (1996) Biochemistry 35, 7559-7565], the helices may function to regulate the kinetics and energetics of ligand binding.

Amino Acid Sequence↗
PubMed2003

Beta-thalassemia in association with a new delta-chain hemoglobin variant [delta116(g18)Arg-->Leu]: implications for carrier screening and prenatal diagnosis.

We describe a complicated genetic counseling and prenatal diagnostic case involving an East Indian couple that had lost two consecutive pregnancies. Hemoglobinopathy screening was conducted to investigate the possibility of Hb Bart's hydrops fetalis or Hb H hydrops fetalis. The initial work-up indicated that alpha-thalassemia was not a contributing factor, with both parents being carriers of single gene deletions (-alpha(3.7)/alphaalpha). However, the Hb electrophoresis results indicated that the couple might be at risk for having children with Hb E/Hb Lepore disease. Subsequent DNA testing demonstrated that the father carried the Hb E mutation, but failed to confirm that the mother carries the Hb Lepore deletion. Sequence analysis revealed that the mother was heterozygous for a common East Indian beta(0)-thalassemia mutation, yet had a normal level of Hb A(2). The mother also carried a previously unreported missense mutation of the delta-globin gene, in cis with the beta(0)-thalassemia mutation, which gave rise to the minor Hb variant originally misidentified as Hb Lepore. This case illustrates the importance of comprehensive molecular analyses for accurate assessment of genetic risks for hemoglobinopathy syndromes.

Abortion, Spontaneous↗
PubMed2000

Astrocytes express specific variants of CaM KII delta and gamma, but not alpha and beta, that determine their cellular localizations.

Multiple isoforms of type II Ca(2+)-calmodulin-dependent kinase (CaM KII) are composed of two major neuron-specific subunits, designated alpha and beta, and two less well-characterized subunits that are also expressed in non-neuronal tissues, designated delta and gamma. Regulated expression of these 4 gene products, and several variants produced by alternative splicing, shows temporal and regional specificity and influences intracellular targeting. We used immunoblotting and RT-PCR to analyze subunit and variant expression and distribution in cultured cerebellar astrocytes and neurons, and whole cerebellar cortex from rodent brain. The data indicate that: (i) astrocytes express a single splice variant of delta, namely delta(2); (ii) like neurons, astrocytes express two forms of CaM KII gamma; gamma(B) and gamma(A); (iii) these CaM KII variants are enriched in the supernate fraction in astrocytes, and the particulate fraction in neurons; (iv) unlike neurons, astrocytes do not express detectable levels of alpha or beta subunits or their respective splice variants. The results indicate that neurons and astrocytes express distinct CaM KII subunits and variants that localize to distinct subcellular compartments and, by inference, exert distinct cellular functions.

Animals↗
PubMed1993

Delta elk-1, a variant of elk-1, fails to interact with the serum response factor and binds to DNA with modulated specificity.

The ets oncogene superfamily codes for a family of transcriptional factors that are involved in gene regulation not only by autonomous DNA binding but also by indirect DNA binding through interaction with cellular factors. We have previously shown that a member of this superfamily, elk-1, is a sequence specific transcriptional activator, which forms a serum response factor (SRF) dependent ternary complex with serum response element (SRE) similar to p62TCF. We describe here an alternatively spliced variant of elk-1 named delta elk-1, which has lost the SRF interaction domain, negative regulatory DNA binding domain, and part of the elk-1 DNA binding domain. This variant elk-1 protein has lost the capacity to form a SRF dependent ternary complex with SRE and to activate fos transcription. Since this splice variant lacks part of the ets DNA binding domain, it binds to DNA with a specificity that is different from that of the full length elk-1 protein. Therefore differential splicing within the DNA binding and protein-protein interaction domains of transcriptional factors can generate proteins with modulated DNA binding specificities and transcriptional regulation. Thus it is conceivable that variant elk-1 might function by competing for some of the elk-1 target sequences (like SRE) and thereby block the transcriptional activation of fos by SRF and elk-1. Alternately, variant elk-1 protein may be the repressor, recruited by the SRE bound SRF for c-fos repression, or it may have an altogether different function. Therefore, elk-1 appears to fall in the category of genes that encode activators and repressors through the mechanism of differential splicing.

3T3 Cells↗
PubMed1995

Differential expression of estrogen receptor mRNA splice variants in the tamoxifen resistant human breast cancer cell line, MCF-7/TAMR-1 compared to the parental MCF-7 cell line.

Breast cancer patients with an estrogen receptor (ER) positive tumor can be treated with the anti-estrogen tamoxifen, but development of anti-estrogen resistance is a serious problem. We have analyzed a tamoxifen resistant human breast cancer cell line MCF-7/TAMR-1 for alterations in ER which might explain the tamoxifen resistance. The MCF-7/TAMR-1 cells expressed both wild-type ER mRNA and protein, and by RT-PCR we were able to clone ER cDNAs corresponding to the following mRNA splice variants: ER delta E2, ER delta E4, ER delta E5, ER delta E7 and a new double splice variant lacking both exon 4 and 7 (ER delta E4,7) The existence of the ER delta E4,7 variant was confirmed by RNase protection assay. Semi-quantitative RT-PCR revealed that ER delta E2 mRNA was expressed at a higher level in MCF-7/TAMR-1 cells, whereas the ER delta E5 mRNA was expressed at a significantly lower level in MCF-7/TAMR-1 cells compared with MCF-7 cells. The differential expression of the two ER mRNA splice variants indicates that they may be involved in anti-estrogen resistance, although the present knowledge of their biological function does not provide us with an explanation.

Base Sequence↗
PubMed2006

Renormalization group analysis of polymer cyclization with non-equilibrium initial conditions.

We develop a renormalization group approach for cyclizing polymers for the case when chain ends are initially close together (ring initial conditions). We analyze the behavior at times much shorter than the longest polymer relaxation time. In agreement with our previous work (Europhys. Lett. 73, 621 (2006)) we find that the leading time dependence of the reaction rate k(t) for ring initial conditions and equilibrium initial conditions are related, namely k (ring)(t) proportional, variant t (-delta) and k (eq)(t) proportional, variant t (1-delta) for times less than the longest polymer relaxation time. Here delta is an effective exponent which approaches delta = 5/4 for very long Rouse chains. Our present analysis also suggests a "sub-leading" term proportional to (ln t)/t which should be particularly significant for smaller values of the renormalized reaction rate and early times. For Zimm dynamics, our RG analysis indicates that the leading time dependence for the reaction rate is k(t) approximately 1/t for very long chains. The leading term is again consistent with the expected relation between ring and equilibrium initial conditions. We also find a logarithmic correction term which we "exponentiate" to a logarithmic form with a Landau pole. The presence of the logarithm is particularly important for smaller chains and, in the Zimm case, large values of the reaction rate.

Algorithms↗
PubMed1992

Recombination of nicked DNA knots by gamma delta resolvase suggests a variant model for the mechanism of strand exchange.

Fast and efficient recombination catalyzed by gamma delta resolvase in vitro requires negative DNA supercoiling of plasmid substrates. The current model for recombination suggests that supercoiling is required to drive DNA strand exchange within a synaptic complex by 'simple rotation' of DNA-linked resolvase promoters. Surprisingly, DNA knots are recombined efficiently in the absence of supercoiling, whereby the rate of recombination increases with the number of irreducible DNA segment crossings, or nodes, within each substrate knot. Recombination products contain three knot nodes less than substrates, suggesting that a reduction in writhe drives the reaction. However, the proposed protomer rotation model predicts that writhe is not altered during the process of strand transfer but, instead, is reduced only when a synaptic complex disassembles after strand exchange. I present evidence that recombination of knotted and of linear substrates coincides with a disassembly of synaptic complexes. The results lead to a variant model for strand exchange on non-supercoiled substrates in which a specific disassembly of the synaptic complex, triggered by a reduction in writhe, guides the cleaved DNA into the recombinant configuration.

DNA, Bacterial↗
PubMed2000

Induction and alternative splicing of delta isoform of Ca(2+)/calmodulin-dependent protein kinase II during neural differentiation of P19 embryonal carcinoma cells and during brain development.

Since the expression of Ca(2+)/calmodulin-dependent protein kinase II (CaM kinase II) is regulated during brain development, the developmental change of the enzyme was investigated during the neural differentiation of murine P19 embryonal carcinoma cells. CaM kinase II activity was induced during the differentiation of P19 cells treated with retinoic acid. Expression of the enzyme was induced 2 days after the treatment and maximized at 5 days. The enzyme activity increased about approximately 8-fold. The enzyme protein was shown to differ between differentiated and undifferentiated cells. The delta isoform of CaM kinase II was found as the major isoform in P19 cells by immunoblotting and reverse transcription-polymerase chain reaction (RT-PCR). A total of four and three alternatively spliced variants of delta isoform were detected in P19 cells by RT-PCR analysis and by immunoblotting, respectively. Although multiple alternatively spliced forms have been reported, the major splice variants of delta isoform in differentiated cells were delta l and delta 9 isoforms, which were specifically detected in differentiated cells. In undifferentiated cells, the major splice variant corresponded to delta 2 isoform. These results indicated that the expression of delta isoform of CaM kinase II was induced, and the splicing pattern of the isoform changed, during neural differentiation. Cell type distinctive changes of splicing pattern of delta isoform were also observed not only during differentiation of cultured neuronal cells, but also during development of rat forebrain and cerebellum.

Alternative Splicing↗
PubMed2000

cDNA cloning of an alternative splicing variant of protein kinase C delta (PKC deltaIII), a new truncated form of PKCdelta, in rats.

Recently, an alternative splicing variant of mouse protein kinase C delta (PKC deltaII, GenBank Accession No. AB011812) has been reported which has a 78 bp (26 amino acid) insertion at the caspase-3 recognition sequence in the V3 region of PKC delta (PKC deltaI). We isolated a cDNA encoding a new variant of PKC delta (PKC deltaIII, AF219629), which has a 83 bp insertion at the same site in the V3 region, by RT-PCR using rat testis RNA as a template. In rats, the 83 bp insertion causes inframe termination, and rat PKC deltaIII protein is expressed as a truncated form, having only the regulatory domain without a catalytic domain. Genomic DNA analysis revealed that the difference between mouse PKC deltaII and rat PKC deltaIII is derived from the different sequence at the 5'-splicing donor sites. To investigate the potential functions of the truncated form of PKC delta, rat PKC deltaIII fused to green fluorescent protein (GFP) was expressed in CHO-K1 cells. PKC deltaIII-GFP was localized in the cytoplasm with dot-like accumulation and highly expressed on the plasma membrane, whereas PKC deltaI-GFP is localized homogeneously throughout the cytoplasm, including the nucleoplasm. Stimulation by phorbol ester caused weak translocation of deltaIII-GFP from the cytosol to the plasma membrane. These results suggest that PKC deltaIII may show a dominant negative effect against PKC deltaI, and that the modulation of signal transduction by alternative splicing variant may play a crucial role in the physiological and/or pathological conditions, and the pathogenesis of disease.

Alternative Splicing↗
PubMed1993

An exon 5 deletion variant of the estrogen receptor frequently coexpressed with wild-type estrogen receptor in human breast cancer.

Recent evidence suggests that the expression of estrogen receptor (ER) variants in breast cancer may interfere with wild-type (wt) ER function and be related to tumor progression and resistance to hormone treatment. One of these variants, ER delta E5, lacking that part of the hormone-binding domain encoded by exon 5, has previously been identified in breast tumors with the unusual estrogen receptor negative (ER-) and progesterone receptor positive (PgR+) phenotype and found to possess constitutive and hormone-independent transcriptional activity. Using a ribonuclease protection assay, we analyzed 27 breast tumors and 4 breast cell lines for the presence of this variant. We found the ER delta E5 variant to be expressed, not only in all of three ER-/PgR+ tumors but also in 19 of 20 ER+/PgR+ or ER+/PgR- tumors. Moreover, the variant was always coexpressed with and often in excess of wtER. ER delta E5 was also found in three breast cancer cell lines (MCF7, T47D, and ZR75-1), although to a lesser extent than wtER. A complete absence of both ER delta E5 and wtER was noted in four ER-/PgR- tumors and one normal breast cell line (HBL-100). Thus, our data suggest that the occurrence of ER delta E5 in breast cancer may represent a critical stage in tumor progression to autonomy.

Breast Neoplasms↗
PubMed1999

Identification and functional analysis of novel cAMP response element binding protein splice variants lacking the basic/leucine zipper domain.

Two novel cAMP response element binding protein (CREB) splice variants were found by reverse transcription-polymerase chain reaction cloning by using mouse brain RNA as a template. One splice variant, named Delta-14, lacks 14 nucleotides at the beginning of exon 9 of the CREBDelta isoform. The other, named Delta-35, lacks 35 nucleotides at the beginning of exon 8 of CREBDelta. These nucleotide deletions cause frame shifts for codon usage, producing proteins which conserve the major phosphorylation site (Ser(133)) but lack the basic/leucine zipper domain, which is essential for binding to DNA and to other transcription factors. Both variants are widely expressed in peripheral tissues, but are enriched in brain, thymus, and testis. CREBDelta-14 and Delta-35 variant proteins were expressed by using an in vitro translation system and by transfecting into human embryonic kidney 293 cells. Both variants were detected by a CREB antibody that recognizes the CREBDelta amino terminus, but not by an antibody which recognizes the CREBDelta carboxy terminus, as would be predicted based on the frame shift. Activation of the cAMP pathway increased phospho-CREB immunoreactivity, indicating that these variants are substrates of cAMP-dependent protein kinase. In addition, immunocytochemical analysis demonstrated that CREBDelta-14 and Delta-35 are primarily cytosolic, whereas CREBalpha is predominantly in the nucleus. Finally, expression of CREBDelta-14 or Delta-35 decreased cAMP responsive element-chloramphenicol acetyltransferase reporter activity, demonstrating that both can function as repressors of endogenous CREB.

Alternative Splicing↗
PubMed2002

Protection of DNA by alpha/beta-type small, acid-soluble proteins from Bacillus subtilis spores against cytosine deamination.

Spores of Bacillus subtilis contain high levels of proteins, termed alpha/beta-type small, acid-soluble proteins (SASP), that protect the spore's DNA against different types of DNA damage. We tested one such protein, SspC, and two of its variants for their ability to protect plasmid DNA against hydrolytic deamination of cytosine to uracil. If unrepaired, such damage to DNA causes C to T mutations. We found that one SspC variant, SspC(Delta 11-D13K), protected DNA against cytosine deamination at two different temperatures (45 and 70 degrees C) and pH values (5.2 and 7.9), reducing the rate of deamination by as much as 10-fold. At 70 degrees C, pH 7.9, the wild-type SspC and its variant, SspC(Delta 11), provided little protection against deamination but were effective in protecting DNA at 45 degrees C, pH 7.9. Parallel studies of the abilities of these proteins to protect DNA against restriction digestion revealed that there was a good correlation between the abilities of the proteins to protect against restriction endonucleases and reductions in cytosine deaminations. These results show that the binding of SspC variants to DNA can prevent attack on DNA bases by water and suggest a new general mechanism by which DNA-binding proteins in cells may be able to protect chromosomes from endogenous and exogenous reactive chemicals by excluding them from the vicinity of DNA.

Bacillus subtilis↗
PubMed1988

Clinical, haematological, and genetic studies of type 2 normal Hb A2 beta thalassaemia.

The clinical and haematological phenotype as well as chain synthesis data were studied in 35 doubly heterozygous patients with either normal Hb A2 and Hb F, type 2 beta thalassaemia and beta (high A2) thalassaemia (26 patients), or type 2 and other rare beta or delta beta variants (nine patients). Patients doubly heterozygous for type 2 and beta zero or delta beta zero thalassaemia variants had no detectable Hb A, indicating that the type 2 normal A2 beta thalassaemia is primarily the result of a beta zero gene. The clinical phenotype varied from severe thalassaemia major to mild thalassaemia intermedia, and was mainly related to the thalassaemia variant with which the type 2 normal A2 beta thalassaemia was combined, and the proportion of Hb A produced in beta + thalassaemia patients. Haematological and chain synthesis data were similar in heterozygotes with type 2 and beta zero or beta + (high A2) thalassaemia. Hb A2 levels were within the normal range (2.3 to 3.6%) though absolute values (Hb A2 per RBC) ranged from low normal (0.5 pg/RBC) to increased levels (1.0 pg/RBC.) The variation of Hb A2, as well as the presence of Hb A2 in a type 2/delta beta high F patient and the complete absence of HbA2 in a homozygous type 2 patient, indicate that there are at least two genotypes of type 2, one beta zero and the other delta beta zero. This has been recently proven by gene mapping studies. For clinicians, routine haematological and family studies are sufficient for the proper treatment and prevention of doubly heterozygous type 2 patients.

Blood Protein Electrophoresis↗
PubMed2024

Infection kinetics, syncytia formation, and inflammatory biomarkers as predictive indicators for the pathogenicity of SARS-CoV-2 Variants of Concern in Calu-3 cells.

The ongoing COVID-19 pandemic has led to the emergence of new SARS-CoV-2 variants as a result of continued host-virus interaction and viral genome mutations. These variants have been associated with varying levels of transmissibility and disease severity. We investigated the phenotypic profiles of six SARS-CoV-2 variants (WT, D614G, Alpha, Beta, Delta, and Omicron) in Calu-3 cells, a human lung epithelial cell line. In our model demonstrated that all variants, except for Omicron, had higher efficiency in virus entry compared to the wild-type. The Delta variant had the greatest phenotypic advantage in terms of early infection kinetics and marked syncytia formation, which could facilitate cell-to-cell spreading, while the Omicron variant displayed slower replication and fewer syncytia formation. We also identified the Delta variant as the strongest inducer of inflammatory biomarkers, including pro-inflammatory cytokines/chemokines (IP-10/CXCL10, TNF-α, and IL-6), anti-inflammatory cytokine (IL-1RA), and growth factors (FGF-2 and VEGF-A), while these inflammatory mediators were not significantly elevated with Omicron infection. These findings are consistent with the observations that there was a generally more pronounced inflammatory response and angiogenesis activity within the lungs of COVID-19 patients as well as more severe symptoms and higher mortality rate during the Delta wave, as compared to less severe symptoms and lower mortality observed during the current Omicron wave in Thailand. Our findings suggest that early infectivity kinetics, enhanced syncytia formation, and specific inflammatory mediator production may serve as predictive indicators for the virulence potential of future SARS-CoV-2 variants.

Humans↗