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At least 469 records · Page 26Linked to original sources
PubMed1999

Identification of a novel splice variant of heat shock cognate protein 70 after chronic antidepressant treatment in rat frontal cortex.

In this study, we identified a novel splice variant of 70-kDa heat shock cognate protein (HSC70), while screening differentially expressed molecules in rat brain after chronic antidepressant treatment. This clone, named HSC49, lacked 470 bp of nucleotides of rat HSC70. HSC49 encoded 442 amino acid residues with a calculated molecular mass of 48.6 kDa. DNA sequence analysis revealed that HSC49 lacked the entire Exon 7 and Exon 8 of the HSC70 gene. Chronic treatment with antidepressant, imipramine or sertraline, induced a 38.5 or 22.5% increase in mRNA levels in rat frontal cortex, respectively, when compared to controls. Western blot analysis also revealed that the protein expression of HSC49 was increased after antidepressant treatment. Our data suggest that HSC49 may be one of the common molecules induced after chronic antidepressant treatment.

Alternative Splicing↗
PubMed2001

Identification of three new splice variants of the SNARE protein SNAP-23.

SNAP-23 has an important role in protein-trafficking processes in mammalian cells and until yet two isoforms of SNAP-23 (SNAP-23a and SNAP-23b) have been described. In the present report, we have identified the existence of three new SNAP-23 isoforms (named SNAP-23c, SNAP-23d, and SNAP-23e), which arise from alternative splicing. By RT-PCR all five splice variants were shown to be expressed in four different human inflammatory cells (eosinophils, basophils, neutrophils, and peripheral blood mononuclear cells). Transfection of the human basophilic KU-812 cell line with plasmid constructs containing the cDNAs of the five splice variants located SNAP-23a and SNAP-23b primarily in the plasma membrane. The other three splice variants were localized both intracellularly and in the plasma membrane.

Alternative Splicing↗
PubMed2000

Genomic organization of human neuropilin-1 and neuropilin-2 genes: identification and distribution of splice variants and soluble isoforms.

Neuropilin-1 (NRP1) and neuropilin-2 (NRP2) are both receptors for semaphorins, which regulate neuronal guidance, and vascular endothelial growth factor (VEGF), an angiogenic factor. The two human NRP1 and NRP2 genes were cloned, and the exon-intron boundaries were determined. The NRP1 and NRP2 genes span over 120 and 112 kb, respectively, and are composed of 17 exons. Five of the exons are identical in size in the two genes, suggesting that they arose by gene duplication. Both NRP genes are characterized by multiple alternatively spliced variants. Two NRP2 isoforms, NRP2a and NRP2b, were cloned. A striking feature of these two isoforms is that they have identical extracellular domains but have divergent transmembrane and cytoplasmic domains. In these domains, NRP2a is closer in sequence identity to NRP1 than to NRP2b. As determined by Northern blot analysis, both NRP2a and NRP2b are expressed in a variety of tissues, mostly in a nonoverlapping manner. Within NRP2a and NRP2b, there are several alternatively spliced species: NRP2a(17), NRP2a(22), NRP2b(0), and NRP2b(5). In addition to full-length NRPs, there are truncated NRPs as well, which contain only the extracellular a/CUB and b/coagulation factor domains. These genes encode proteins that are soluble (sNRP) and released by cells. In addition to s12NRP1, which was previously cloned, s11NRP1 and s9NRP2 have now been cloned. These sNRP molecules are characterized by having intron-derived sequences at their C-termini. Altogether, eight NRP isoforms are described in this report. It was concluded that there are multiple NRP1 and NRP2 isoforms including intact and soluble forms. Characterization of these isoforms should help to elucidate the function of NRPs in neuronal guidance and angiogenesis.

Amino Acid Sequence↗
PubMed2001

Amino acid substitution(s) in the stem-anchor region of langat virus envelope protein attenuates mouse neurovirulence.

The identification of variants that are unable to bind membrane receptor preparations (MRPs) has previously been shown to select attenuated yellow fever and Japanese encephalitis viruses. In this study, this methodology has been extended to the tick-borne serocomplex of flaviviruses. Langat (LGT) virus strain TP21 was bound to mouse or human brain MRPs and viruses that escaped binding were isolated and characterized. In addition, variant viruses escaping neutralization by the monoclonal antibody (MAb) 9F9 were also isolated. All of the variant viruses were attenuated for mouse neurovirulence (> or =13-fold). Sequence analysis of the prM/E region of the variant viruses identified mutations within the stem-anchor region of the E protein in variants isolated following incubation with mouse or human brain MRPs at a pH > or = 7.0. The MAb 9F9 variants and MRP variants isolated at pH 5.0, which should induce a conformational shift in the viral E protein, had nearly identical mutations in the prM/M protein immediately N-terminal to the prM/E cleavage site. MAb 9F9 neutralized none of the variant viruses and hemagglutination inhibition assays suggest that the variant virus surface proteins have slightly different conformations compared to the parental virus. These data support previous work indicating that the stem-anchor region of the E protein is important to the surface architecture of the tick-borne flaviviruses. In addition, this study demonstrates that the M protein is at least partially solvent accessible on the virion surface and that the M protein plays a role in maintaining the conformation of the M/E surface complex.

Amino Acid Sequence↗
PubMed1992

Apolipoprotein genes and atherosclerosis.

In order to elucidate the genetic abnormalities underlying lipoprotein disorders associated with coronary heart disease susceptibility, researchers have looked for candidate genes. The studies have focused particularly on the lipoprotein transport genes. Relatively common as well as rare mutations have already been identified in several of these genes. In addition, further metabolic and genetic studies indicate that some of these loci harbor significant, but as yet undefined, genetic variation. In the next few years, it is not unreasonable to expect that all or most of the significant mutations at these loci will be catalogued. It is too early to know whether this will be sufficient to explain the genetic basis of altered lipoprotein levels or whether new loci will need to be investigated. Additional candidate gene loci might be those coding for genes involved in intracellular cholesterol metabolism, cholesterol absorption, or insulin resistance. New loci may also be revealed by the technique of reverse genetics. A more complete understanding of the genetics of atherosclerosis susceptibility will probably also entail the identification of variants at genetic loci that control both the reaction of the blood vessel wall to atherogenic lipoproteins and the thrombosis system. Investigation of the genetic basis of coronary heart disease susceptibility remains a worthwhile and lively field, with important clinical and public health ramifications.

Cholesterol↗
PubMed1980

Immuno-overlay: a method for identification of hepatoma cell colonies that secrete albumin.

A screening technique was developed for the identification of clones of hepatoma cells that secrete albumin. The technique employs the overlay of a 1% agarose solution containing antiserum to albumin onto clones of hepatoma cells. A distinct immunoprecipitation complex is formed in the immuno-overlay that corresponds directly to the position of each secreting clone. Clones deficient in albumin secretion do not form an immunoprecipitate. Thus comparison of the immuno-overlay and the cell colonies results in identification of variant clones as well as those capable of secretion. Biochemical characterization of the region of agarose overlay from secreting and nonsecreting clones demonstrates the specificity of the method and its potential for selection of colonies that are secreting other hepatic or cellular proteins.

Albumins↗
PubMed2006

Paraoxonase 2 (PON2) polymorphisms and development of renal dysfunction in type 2 diabetes: UKPDS 76.

AIMS/HYPOTHESIS: Identification of variants predicting development of renal dysfunction would offer substantial clinical benefits. There is evidence that coding non-synonymous variants in the gene encoding paraoxonase 2 (PON2) are associated with nephropathy in both type 1 and type 2 diabetes. METHODS: We examined the relationship between variation at the C311S and A148G polymorphisms (together with PON2 intronic variant rs12704795) and indices of renal dysfunction (progression to micro- and macroalbuminuria, plasma creatinine increases) in 3,374 newly diagnosed type 2 diabetic subjects from the UK Prospective Diabetes Study followed prospectively (median 14.0 years), using proportional hazards models, adjusted for sex, ethnicity and other known or putative risk factors. RESULTS: rs12704795 genotypes were associated with differing rates of development of microalbuminuria (relative risk [RR] for CC vs AA homozygotes 0.68 [95% CI 0.54-0.87], p=0.002) but not other measures of worsening renal function. Heterozygotes for C311S were more likely to develop microalbuminuria (RR=1.31 [95% CI 1.11-1.54], p=0.001) but less likely to double creatinine levels during follow-up (RR=0.49 [95% CI 0.27-0.89], p=0.02). There was no corroboration of this latter association for related outcomes and no prior evidence supports heterosis effects at this locus. CONCLUSIONS/INTERPRETATION: We conclude that the PON2 variants typed in this study have, at best, a small effect on the risk of renal dysfunction in type 2 diabetes.

Albuminuria↗
PubMed1997

Identification of four trp1 gene variants murine pancreatic beta-cells.

Insulin secretion is stimulated by glucose, hormones and neurotransmitters. Both activation of a non-selective cation current and activation of a Ca2+ current in response to depletion of intracellular Ca2+ stores have been suggested to play a role in this stimulation. The properties of these currents resemble those reported for the Drosophila genes trp and trpl. Using the reverse transcription polymerase chain reaction and Northern blot analysis we found that of the six mammalian trp-related genes (trp1-6), only trp1 was expressed at high levels in the mouse insulinoma cell line MIN6. We cloned the murine homologue of human trp1 from MIN6 cells and identified four variants (alpha, beta, gamma and delta), generated by alternative splicing near the N-terminus of the protein. In vitro translation showed that only the alpha and beta splice variants are efficiently expressed. The beta variant is the dominant form in MIN6 cells (and probably in mouse pancreatic islets), whereas the alpha variant is the major type in the mouse brain. The beta variant showed 99% identity to the human homologue at the amino acid level.

Alternative Splicing↗
PubMed2005

Large-scale identification and characterization of genetic variants in asthma candidate genes.

Asthma is a chronic inflammatory disorder of the airways, and a number of genetic loci are associated with the disease. Candidate gene association studies have been regarded as effective tools to study complex traits. Knowledge of the sequence variation and structure of the candidate genes is required for association studies. Thus, we investigated the genetic variants of 32 asthma candidate genes selected by colocalization of positional and functional candidate genes. We screened all exons and promoter regions of those genes using 12 healthy individuals and 12 asthma patients and identified a total of 418 single nucleotide polymorphisms (SNPs), including 270 known SNPs and 148 novel SNPs. Levels of nucleotide diversity varied from gene to gene (0.72 x 10(-4)-14.53 x 10(-4)), but the average nucleotide diversity between coding SNPs (cSNPs) and noncoding SNPs was roughly equivalent (4.63 x 10(-4) vs 4.69 x 10(-4)). However, nucleotide diversity of cSNPs was strongly correlated to codon degeneracy. Nucleotide diversity was much higher at fourfold degenerate sites than at nondegenerate sites (9.42 x 10(-4) vs 3.14 x 10(-4)). Gene-based haplotype analysis of asthma-associated genes in this study revealed that common haplotypes (frequency >5%) represented 90.5% of chromosomes, and they could be uniquely identified with five or fewer haplotype-tagging SNPs per gene. Therefore, our results may have important implications for the selection of asthma candidate genes and SNP markers for comprehensive association studies using large sample populations.

Asthma↗
PubMed2005

Identification and characterization of novel variants of the thioredoxin reductase 3 new transcript 1 TXNRD3NT1.

We have identified and characterized a new gene sequence, TXNRD3NT1, whose transcripts, corresponding to the EST AA430236, were found by Affymetrix DNA chip analysis to be significantly down regulated in affected psoriatic tissue. The full-length cDNA of TXNRD3NT1 was isolated and characterized by combining 5'- and 3'-RACE (rapid amplication of cDNA ends) with screening a keratinocyte cDNA library, designing appropriate PCR primers, cloning amplified products, sequencing, and sequence analysis. Because part of this gene overlaps the previously described thioredoxin reductase 3 (TXNRD3) gene, we have named it TXNRD3NT1 (TXNRD3 new transcript 1). The full-length TXNRD3NT1 cDNA has 1133 nucleotides with a 251-bp 3-UTRand 2 poly(A)signal variants and 2 poly (A) sites. The TXNRD3NT1 cDNA ORF encodes for 133 amino acids, with the first four residues coding for a tubulin-beta mRNA autoregulation signal. Mapping the cDNA nucleotide sequence to the human genome sequence revealed that the TXNRD3NT1 gene has 4 exons located on Chromosome 3, at position 3q21. Exons 1 and 2 of the TXNRD3NT1 gene overlap with exons 15 and 16 of the thioredoxin reductase 2 gene which has different ORFs to that of TXNRD3NT1. The translation initiation codon ATG was found in exon 3 of the TXNRD3NT1 gene. RT-PCR showed that the full-length variant of the TXNRD3NT1 gene was expressed in only four issues (pancreas, esophagus, bone marrow, and keratinocytes) of the 30 different tissues tested. In most other tissues, an aberrant and truncated form of the transcript (i.e., missing exon 3 and part of exon 4) was detected. The result of a preliminary association study between psoriasis and single microsatellite marker of the TXNRD3NT1 gene suggests that it may not be a significant genetic determinant of psoriasis. However, we cannot exclude the possibility that other sequence variants may still exist within the TXNRD3NT1 gene. Sequence analysis of the TXNRD3NT1 gene from 8 psoriasis patients and 8 healthy controls revealed a number of synonymous SNPs that may be useful markers for future disease association studies.

Alternative Splicing↗
PubMed2006

Cloning, comparative characterization of porcine SCAP gene, and identification of its two splice variants.

Sterol responsive element binding protein (SREBP) cleavage-activating protein (SCAP) is the key regulator of activation of SREBPs, which stimulate most enzymes in cholesterol and lipid synthesis. In order to investigate the molecular basis of lipid metabolism in the pig, a unique model for fat deposition, we isolated and characterized the porcine SCAP. The 4,096-bp full-length porcine SCAP cDNA contains an open reading frame of 3,840 bp. The predicted SCAP protein consists of 1,280 amino acids of 55-92% identity with its vertebrate counterparts. The porcine SCAP gene consists of at least 19 exons and 18 introns, which span over 13 kb of the genome. The porcine SCAP gene was mapped to chromosome 13q21-22 using a porcine-rodent somatic cell hybrid panel. Comparison of SCAP genomic structures from various species revealed intron losses in porcine, Tetraodon and fugu SCAP, and intron gains in cow and chicken SCAP. Moreover, we isolated two novel splicing SCAP variants with 193-bp (variant 2) in-frame deletion from testis and a variant with 291-bp (variant 3) in-frame deletion from liver and muscle, which may affect the function of the porcine SCAP. In conclusion, the intron gains and losses appear to have contributed to the shape of the modern SCAP family. The splice variants detected, first to be reported in any species, may be involved in the particulars of the fat metabolism in the pig. Our data lay foundation for further study of SCAP function in this species.

Alternative Splicing↗
PubMed2001

Use of gene markers to guide antihypertensive therapy.

Sequencing of the human genome has elevated the potential for genetic information to aid in the prevention, diagnosis, and treatment of common chronic diseases. One beneficial application of genetic information is the identification of variants that influence response to pharmaceutical agents used to lower blood pressure and prevent target organ complications of hypertension. Knowledge of genetic variants that influence blood pressure response to antihypertensive drugs may allow more individualized tailoring of antihypertensive drug therapy, and provide greater insight into the molecular mechanisms regulating blood pressure levels and causing hypertension.

Antihypertensive Agents↗
PubMed2025

Identification of four novel ACADVL variants in eight Chinese unrelated patients with very long-chain acyl-CoA dehydrogenase deficiency.

BACKGROUND: Very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) is a disorder of mitochondrial fatty acid oxidation with an autosomal recessive manner and is due to the VLCAD enzyme deficiency which is encoded by the ACADVL gene. The purpose of this study was to elucidate the clinical manifestations and analyze the molecular findings of eight Chinese patients with VLCADD. METHODS: We investigated eight Chinese VLCADD patients (three males, five females) from eight unrelated families. Molecular analysis was performed under the application of next-generation sequencing (NGS) in combination with Sanger sequencing validation to confirm the likely pathogenic variants in these patients. RESULTS: Patient 1 (P1) exhibited the most severe clinical features and passed away 3 h after admission on the second day of life. Unfortunately, P2 succumbed to hypoketotic hypoglycemia at 5 months of age. Except for asymptomatic P7, the remaining patients also developed clinical presentations of varying severity at different ages. Molecular data revealed that all affected individuals were compound heterozygotes for ACADVL variants. A total of 14 variants (4 novel and 10 known) were identified and the pathogenicity was evaluated based on the American College of Medical Genetics and Genomics (ACMG) criteria and different in silico prediction tools. CONCLUSIONS: The analysis of genotype-phenotype relationships preliminarily suggests that the compound heterozygous variants identified in these patients are likely the primary cause of VLCADD. Our study expands the mutation spectrum of ACADVL and highlights the significance of genetic analysis in early diagnosis and therapeutic intervention of monogenic hereditary diseases especially those with rapid disease progression.

Female↗
PubMed2026

Optimization of a Semi-nested PCR Protocol for Amplifying the Entire Spike Protein Region to Identify SARS-CoV-2 Variants in Wastewater.

Wastewater-based monitoring of SARS-CoV-2 and other pathogens is a widely adopted tool for assessing epidemic dynamics. While quantitative assays are commonly used to estimate infection levels in catchment populations, phylogenetic information-such as identifying circulating variants-is also crucial for public health. However, applying the widely used ARTIC protocol for full-genome sequencing to wastewater samples has proven challenging, likely due to the limited specificity and sensitivity of multiplex RT-PCR in such complex matrices. In this study, we developed and optimized a semi-nested RT-PCR assay targeting the full S-protein coding region (~4000 bases) for phylogenetic characterization of SARS-CoV-2 in wastewater. By reducing multiplexing and using single-plex reactions for both RT and PCR steps, we successfully amplified ~2000&#xa0;bp fragments. Amplicons were sequenced using the Flongle Flow Cell platform. The optimized method-consisting of reverse transcription with specific primers followed by three parallel single-plex semi-nested PCRs-yielded over 1,000 SARS-CoV-2-like reads per primer set in 30 out of 39 wastewater samples in treatment plants in Japan, including those with <10 copies per analyte. Variant proportions were estimated using a newly developed approach based on single-nucleotide variant pattern matrix, revealing the presence of multiple co-circulating variants, including XBB lineages, JN.1, and notably BA.2.75, which was undetected in domestic clinical surveillance. These results highlight the effectiveness of our approach for detecting temporal shifts in SARS-CoV-2 variants, even at low RNA concentrations.

Polymerase Chain Reaction↗
PubMed1986

Histone separation by high-performance liquid chromatography on C4 reverse-phase columns.

Previous work in our laboratory (Lindner, H., Helliger, W., and Puschendorf, B. (1986) J. Chromatogr. 357, 301-310) described a rapid separation of H1 and core histones by reverse-phase high-performance liquid chromatography using a Bio-Rad Hi-Pore butyl (C4) silica-based column. Despite the short elution time, a high resolution of the different histone fractions, except H4 and H2A (MHP), could be obtained. In this report we present a method for the separation of H4 and H2A (MHP) as well, while maintaining a similar analysis time. By varying the gradient, trifluoroacetic acid concentration (0.05%), and flow rate (1.3 ml/min) the histones were eluted from the C4 column in the following order: H1 (MHP), H1 (LHP), H2B, H2A (LHP), H4, H2A (MHP), H3 (LHP), and H3 (MHP). LHP and MHP refer to less and more hydrophobic histone variants. The identification of the individual protein fractions was performed by comparison the retention times with pure histone markers as well as by gel electrophoresis.

Animals↗
PubMed1994

Alpha-(2-->3)- and alpha-(2-->6)-sialyltransferase activities present in three variants of Ehrlich tumor cells: identification of the products derived from N-acetyllactosamine and beta-D-Gal-(1-->3)-alpha-D-GalNAc-(1-->O)-Bn.

We compared several sialytransferase activities related to synthesis of O-linked and N-linked sialyglycoproteins in Ehrlich ascites tumor cells that grow normally in murine ascites, but are not adherent nor grow in tissue culture (na-EAT cells), with those in cells that were selected to grow in tissue culture and adhere to extracellular matrices (a-EAT cells). Crude Golgi preparations from both cell types contained predominantly beta-D-Gal-(1-->3)-D-GalNAc alpha-(2-->3)-sialyltransferase activity. Sialylation of N-acetyllactosamine, lacto-N-tetraose, and benzyl alpha-D-GalNAc occurred at from 1 to 4% of that activity. Analysis, by ion-exchange HPLC at high pH, of sialylated N-acetyllactosamine showed that na-EAT cells sialylated beta-D-Gal-(1-->4)-D-GlcNAc mostly by alpha-(2-->3)-sialyltransferase, whereas beta-D-Gal-(1-->4)-D-GlcNAc alpha-(2-->6)-sialyltransferase activity was prominent in a-EAT cells. In addition, preparations from na-EAT cells formed significant quantities of an unknown tritiated product from CMP-[9-3H]sialic acid, suggesting at least one other difference in enzyme levels between the cell types. a-EAT cells reestablished in murine ascites for 11 passages retained the sialyltransferase levels characteristic of a-EAT cells. When viable cells were labeled with D-[3H]glucosamine, na-EAT cells formed larger amounts of sialic acid in O-linked glycoproteins than did a-EAT cells.

Amino Sugars↗
PubMed1992

Identification of a novel transthyretin variant (Val30----Leu) associated with familial amyloidotic polyneuropathy.

A novel variant transthyretin which contains a leucine-for-valine substitution at position 30 was isolated and identified in the serum of a patient with familial amyloidotic polyneuropathy (FAP). The amino acid substitution was proven to result from a guanine-to-cytosine change at the first base of codon 30 located in exon 2 in the mutated transthyretin gene by restriction fragment length analysis on the amplified transthyretin gene using Cfr13 I. The study indicates that the point mutation of the transthyretin gene is a cause of the disorder.

Amino Acid Sequence↗