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At least 1,423 records · Page 79Linked to original sources
PubMed1998

Differentiation of F18ab+ from F18ac+ Escherichia coli by single-strand conformational polymorphism analysis of the major fimbrial subunit gene (fedA).

Toxin-producing Escherichia coli expressing F18 fimbriae colonizes the small intestines of weaned pigs and causes diarrhea, edema disease, or both. The F18 family is composed of two antigenic variants, F18ab and F18ac. Because many strains do not express F18 fimbriae in vitro, identification and differentiation of these two variants are difficult. Single-strand conformational polymorphism (SSCP) analysis is a rapid method for identifying genetic mutations and polymorphisms. The F18 major fimbrial subunit genes (fedA) of 138 strains were amplified by PCR, and genetic differences were detected by SSCP analysis. The SSCP analysis of the fedA gene differentiated F18ab+ strains from F18ac+ strains. Most strains classified as F18ab+ by SSCP analysis contained Shiga toxin 2e and enterotoxin genes. Most strains classified as F18ac+ by SSCP analysis contained only enterotoxin genes. The SSCP analysis was a useful method for predicting the antigenicity of F18+ E. coli and could also be used for analysis of other virulence genes in E. coli and other pathogenic bacteria.

Amino Acid Sequence↗
PubMed1993

Experimentally produced pulmonary arterial occlusion in the dog: identification with pertechnegas inhalation.

Pertechnegas, a variant of technegas, is a fine, dry aerosol formed when technetium-99m pertechnetate is vaporized in a technegas generator under appropriate conditions. After inhalation, the aerosol is deposited almost entirely on the surfaces of terminal respiratory structures. Unlike technegas, however, pertechnegas crosses the alveolar-capillary membrane and leaves the lung through the pulmonary circulation. To demonstrate prolonged retention of pertechnegas in regions of lung supplied by an occluded pulmonary artery, 12 pulmonary arterial occlusions were experimentally produced in two dogs. After inhalation of pertechnegas, a transient focus of increased pulmonary radioactivity was seen in 11 occlusions; 10 of these 11 foci were easily confirmed by means of subsequent perfusion scintigraphy. All 11 foci of retained pertechnegas corresponded to the location of the non-perfused lung. Thus, it is possible to identify ischemic lung with focal retention of pertechnegas (a finding that indicates preserved ventilation but diminished perfusion) by use of a single examination.

Aerosols↗
PubMed1996

[The grouping of morphological variants of non-Hodgkin's lymphomas (lymphosarcomas) by the degree of malignancy].

The authors stated that WHO classification allows identification of two groups of morphological variants of non-Hodgkin's lymphomas: low- and high-grade malignancy. These differ by principal clinical characteristics, incidence of complete and partial remissions, survival duration. The analysis of clinical course, long-term and short-term treatment outcomes is provided for 674 patients with the above lymphomas.

Adolescent↗
PubMedDate not supplied

[Determining a variant of skeletal massiveness and probable type of build in human identification by bone remnants].

A simple algorithm for predicting the somatic type by bone rudiments is developed on the basis of measurements of 70 adult male skeletons by 13 parameters of 4 long tubular bones and the data on Russian populations, residents of middle Russia and Transbaikal territory, with visually evaluated constitution types (n = 360). The procedure consists of 2 stages. At first the massiveness of the skeleton is evaluated: A) gracial; B) stiphroidal; C) theinoidal; and D) massive. For this, a combination of the value and sign of the main components are used, which are obtained using estimation equations for different combinations of 4 long tubular bones of the limbs. Then using a special table reflecting the mutual incidence of both constitutional categories, the most probable somatic type is determined by the variant of the skeleton massiveness. The effect of the type of skeletal system development on the manifestation of other morphological signs was also taken into consideration. Complete description of variants of skeleton massiveness, based on available data, is presented.

Algorithms↗
PubMed2025

OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.

MOTIVATION: Structural variants (SVs) influence gene regulation, disease progression, and diagnostics, yet integrating SV calls across platforms remains difficult due to inconsistent annotations, limited merging flexibility, and fragmented workflows. Ambiguous breakend (BND) annotations, which comprise many variant calls, are often discarded or misclassified, hindering variant characterization. Existing tools lack advanced merging operations essential for precise identification of disease-specific or somatic variants across samples or patient groups. Additionally, current SV analysis pipelines require extensive manual intervention and complex parameter tuning, compromising reproducibility and scalability. Addressing these gaps is crucial for improving the accuracy, interpretability, and clinical utility of SV analyses. RESULTS: We developed OctopuSV and TentacleSV to address these long-standing challenges in SV analysis. OctopuSV features a specialized BND correction module that converts ambiguous BND annotations into canonical SV types, recovering important variants that are often overlooked by existing tools. Additionally, it provides advanced set operations (difference, complement, custom-defined) that enable sophisticated variant filtering without programming expertise, critical for identifying tumor-specific SVs or variants unique to specific sample groups. TentacleSV completes our solution by automating the entire SV analysis process from raw sequencing data to high-confidence callsets, ensuring consistency and reproducibility across projects. Benchmarking across short-read and long-read platforms showed superior F1 score, complete SV type consistency compared to existing tools. Our framework enables experimental biologists and clinical researchers to perform sophisticated analyses ranging from cancer subtype-specific SV identification to multi-sample comparative studies without requiring specialized programming skills. AVAILABILITY AND IMPLEMENTATION: All codes are available at https://github.com/ylab-hi/OctopuSV; https://github.com/ylab-hi/TentacleSV.

Software↗
PubMed1995

Novel HLA-DPB1 alleles detected in the Ethiopian population.

The number of identified HLA-DPB1 alleles increased rapidly by application of DNA-based typing techniques. PCR-SSO typing indicated the presence of possible new HLA-DPB1 variants in the Ethiopian population. The use of the SBT technique, which considers polymorphic as well as constant regions in the second exon of HLA genes, allowed direct identification of two new allelic variants. Moreover, a recently identified HLA-DPA1 variant was also present in this population. The newly defined allelic HLA-DPB1 sequences found in five individuals of the Ethiopian population were confirmed by cloning and subsequent sequencing of the cloned DNA. One of the new alleles was shown to segregate in a family and was also present in unrelated individuals. Both new DPB1 alleles represent new combinations of existing polymorphism in the hypervariable regions. In different populations the frequency of these new HLA-DP variants remains to be determined.

Alleles↗
PubMed1997

Cell surface localization and density of the tumor-associated variant of the epidermal growth factor receptor, EGFRvIII.

The potential of therapeutic targeting of tumor cell surface epidermal growth factor receptors (EGFRs) by modified ligands or specific antibodies has been limited by the normal tissue distribution of the receptor. The identification and characterization of a variant of this receptor, EGFRvIII, which is not expressed in normal tissues but has been described in gliomas, non-small cell lung carcinomas, and breast carcinomas, has provided a highly specific, internalizing target for antibody-mediated approaches. To determine the feasibility of immunotargeting EGFRvIII, we have assessed the qualitative distribution and quantitative expression at both the population and cellular levels of EGFRvIII in 21 biopsy samples of human gliomas by indirect analytical and quantitative flow cytometry and by immunohistochemical assay of frozen and formalin-fixed tissue. Consistent with previous reports, 50% of gliomas tested (1 of 2 anaplastic astrocytomas, 7 of 12 glioblastoma multiforme, and 2 of 6 oligodendrogliomas) expressed EGFRvIII, as determined by a minimum of 2 separate assays. Minimum estimates of the proportion of positive tumor cells in these populations ranged from 37-86%; in four of five cases in which quantitation of the EGFRvIII density/cell was performed, values of 2.7-6.8 x 10(5) were obtained with monoclonal antibody (mAb) L8A4 (EGFRvIII specific), levels consistent with successful in vivo immunotargeting. Confocal microscopic analysis confirmed that the subcellular localization of EGFRvIII was identical to that described for EGFR: predominant cell membrane expression, with some perinuclear distribution suggestive of localization to the Golgi region. Neither EGFR nor EGFRvIII was found within the nucleus. This study establishes for the first time that approximately 50% of human glioma biopsies contain cell populations expressing a sufficient number of membrane-expressed EGFRvIIIs to mediate specific anti-EGFRvIII mAb localization. Coupled with previous demonstrations of the rapid internalization of specific mAb-EGFRvIII complexes and the susceptibility of the targeted cells to isotope or toxin-mediated cytotoxicity, this study establishes the validity of targeting EGFRvIII for therapy of mutant receptor-positive gliomas, breast carcinomas, and non-small cell lung carcinomas.

Animals↗
PubMed2003

Combinatorial redesign of the DNA binding specificity of a prokaryotic helix-turn-helix repressor.

Redesign of the bacteriophage 434 Cro repressor was accomplished by using an in vivo genetic screening system to identify new variants that specifically bound previously unrecognized DNA sequences. Site-directed, combinatorial mutagenesis of the 434 Cro helix-turn-helix (HTH) motif generated libraries of new variants which were screened for binding to new target sequences. Multiple mutations of 434 Cro that functionally converted wild-type (wt) 434 Cro DNA binding-sequence specificity to that of a lambda bacteriophage-specific repressor were identified. The libraries contained variations within the HTH sequence at only three positions. In vivo and in vitro analysis of several of the identified 434 Cro variants showed that the relatively few changes in the recognition helix of the HTH motif of 434 Cro resulted in specific and tight binding of the target DNA sequences. For the best 434 Cro variant identified, an apparent K(d) for lambda O(R)3 of 1 nM was observed. In competition experiments, this Cro variant was observed to be highly selective. We conclude that functional 434 Cro repressor variants with new DNA binding specificities can be generated from wt 434 Cro by mutating just the recognition helix. Important characteristics of the screening system responsible for the successful identifications are discussed. Application of the techniques presented here may allow the identification of DNA binding protein variants that functionally affect DNA regulatory sequences important in disease and industrial and biotechnological processes.

Bacteriophage lambda↗
PubMed1982

Identification of human CML target. HLA-B locus (B12) antigen variants defined by CTL generated between B locus-identical (B12) responder-stimulator pairs.

The genetics of human CML targets were studied by seven CTL generated in combinations iun which the responder/stimulator difference was limited to one (or two) HLA-A, -B, or -C antigens. Unstimulated peripheral blood lymphocytes were used as targets. CTL sensitized against antigens A11, Aw31, or B17 lysed all cells bearing the respective target from a large panel of cells from unrelated individuals. Hence, at least one CTL clone was directed against the HLA antigen molecule. However, all CTL also exerted cross-kill to cells not sharing the stimulating HLA antigen. For two CTL, the target of the cross-kill was not clarified. Five CTL were found where the cross-kill was directed against antigen HLA-B12 (Bw44 and Bw45). All these cTL were generated in R/S pairs identical for B locus antigens (Bw44/Bw35 heterozygotes). The individual CTL lysed different parts of the panel of B12-positive target cells. The interpretation is that these CTL detect subtypes of HLA antigens, but alternative possibilities are also considered. Four B12 subtypes are described, tentatively designated as B12-related CML targets. Identification of HLA-B-related CML targets represent CML "typing" of HLA-antigen differences that were not detected serologically. The subtypes can now be tested for their possible functional significance.

B-Lymphocytes↗
PubMed2000

A new variant of the gamma subunit of renal Na,K-ATPase. Identification by mass spectrometry, antibody binding, and expression in cultured cells.

The gamma subunit is a specific regulator of Na,K-ATPase expressed mainly in kidney. On SDS-polyacryylamide gel electrophoresis, gamma runs as a doublet, but the origin and significance of the doublet is obscure. Mass spectrometry of the gamma chains of rat kidney Na, K-ATPase shows that gamma(a) (upper) has a mass of 7184.0 +/- 1 Da (carbamidomethyl cysteine), corresponding closely to that for the published sequence without the initiator methionine, while gamma(b) (lower) has a mass of 7337.9 +/- 1Da. Tryptic peptide mapping and sequencing by mass spectrometry reveals that the seven N-terminal residues of gamma(a), TELSANH, are replaced by Ac-MDRWYL in gamma(b), but otherwise the chains are identical. Antibodies raised against peptides TELSANHC and MDRWYLC recognize either gamma(a) or gamma(b) of the Na,K-ATPase, respectively. gamma(a) or gamma(b) cDNAs have been expressed in human embryonic kidney and HeLa cells. The major bands expressed correspond to gamma(a) or gamma(b) of renal Na, K-ATPase. Additional minor bands seen after transfection, namely gamma(a)' in human embryonic kidney and gamma(b)' in HeLa, are presumably cell-specific modifications. The present work clarifies earlier uncertainty regarding doublets seen in kidney and in transfected cells. In particular, the results show that renal Na, K-ATPase contains two variants of the gamma subunit with different sequences but otherwise are unmodified. We discuss the possible functional significance of the two variants.

Amino Acid Sequence↗
PubMed2004

Microsphere bead arrays and sequence validation of 5/7/9T genotypes for multiplex screening of cystic fibrosis polymorphisms.

The development of simple and rapid methods for the detection of the common genetic mutations associated with cystic fibrosis (CF) requires access to positive-control samples including the 5/7/9T variants of intron 8. We used PCR and a simple multiplex bead-array assay to identify 5/7/9T control samples from 29 commercially available DNA samples. Unpurified PCR products were directly hybridized to color-coded beads containing allele-specific capture probes for 5/7/9T detection. The performance of the assay was investigated using reverse-complement oligonucleotides, individual PCR products, and multiplex PCR products for 5/7/9T detection within a complex CFTR screening assay. Samples were genotyped by grouping the relative signal intensities from each capture probe. Of 29 commercially available DNA samples analyzed, 2 5T/7T, 2 5T/9T, 9 7T/9T, 11 7T/7T, and 5 9T/9T genotypes were identified. The genotype within each sample group was confirmed by DNA sequencing. The assay was compatible with the analysis of 10 to 1000 ng of genomic DNA isolated from whole blood and allowed for the separate identification of primary CFTR mutations from reflex variants. The correct identification of positive controls demonstrated the utility of a simple bead-array assay and provided accessible samples for assay optimization and for routine quality control in the clinical laboratory.

Alleles↗
PubMed1990

[Features of mutated changes of genomic RNA of cold-adapted and hr-variants of influenza group A virus, detected by RNA:RNA hybridization].

The presence of mutations in the majority of the genes of cold-adapted strains A/Leningrad/134/17/57 (H2N2), A/Leningrad/134/47/57 (H2N2) and A/PR/8/59/1 (H1N1) of influenza A virus has been demonstrated by the RNA-RNA hybridization with the subsequent electrophoresis of double-stranded RNA in 7.5% polyacrylamide gel. The strains were cultivated 17, 47 and 59 passages in the chicken embryos at 25 degrees C. In the genomes of variants passaged in chicken embryos at optimal temperature of incubation 36 degrees C (hr-variants) the used technique permits identification of a single mutant gene. The obtained data suppose the attenuation of cold-adapted vaccine strains of influenza A virus and their high genetic stability to be a result of selection of the variants obtaining multiple mutations in the genome during passaging of the virions at cold temperature. The attenuation of hr-variants is defined by 1-2 mutations (first of all in HA-gene) that makes understandable their inability to serve as donors for recombinant live influenza vaccines construction.

Antigens, Viral↗
PubMedDate not supplied

[II. Pharmacogenetics--the future of modern pharmacology and genetics].

Pharmacogenetics is a scientific discipline connecting pharmacology and genetics. Its point of interest is an analysis of the variable, genetically determined patient's response to drugs. The basic discovery in this field was the elucidation of the heterogenic response of patients to the tuberculostatic drug -- isoniazid. The new era of searching for the molecular background of the variable drugs metabolism has begun after identification, in the 50's, of the polymorphic variants of NAT2 gene. It encodes for N-acetyltransferase 2, an isoniazid metabolizing enzyme. The key catalysts of the biotransformation reactions are cytochrome P450 isoenzymes. Identification of the polymorphic variants of genes encoding these enzymes enabled an explanation of the heterogenic drugs tolerance. The current knowledge shows that the genetic defects that are responsible for variable pharmacological response concern not only genes encoding the metabolising enzymes but also transporter proteins and drug receptors. Due to achievements of the molecular genetics and putting into practice the modern bioinformatic technics new pharmacological opportunities have been created. It becomes possible to predict the patient's individual reactions and needs, without the necessity of treatment by "trial and error". Pharmacogenetics will allow to implement personalized therapy leading to safer and more effective drugs usage. Identification of the individual metabolising paths will reduce patient's exposition to the side effects of many drugs. In spite of many financial and logistic limitations there are chances of introducing the pharmacogenetic analysis -- as an obligatory step -- to the phases II and III of clinical trials by 2020.

Cytochrome P-450 Enzyme System↗
PubMed1996

Attenuated function of a variant form of the helix-loop-helix protein, Id-3, generated by an alternative splicing mechanism.

The Id family of helix-loop-helix proteins function as negative regulators of DNA binding, basic helix-loop-helix proteins in the regulation of cell growth and differentiation. We report here on the identification of a 17 kDa variant of the 14 kDa Id-3 protein termed Id-3L (long version) which possesses a unique 60 amino acid carboxy-terminus generated by read through of a 'coding intron' and alternative splicing. Northern analysis revealed expression of a minor 1.1 kb Id-3L transcript together with the predominant 0.95 kb Id-3 transcript in the majority of adult human tissues analysed. The variant Id-3L protein is functionally distinguishable from conventional Id-3 since in in vitro DNA mobility shift assays, it was greatly impaired in its ability to abrogate binding of the basic helix-loop-helix protein, E47, to an E box recognition sequence.

Adult↗
PubMed2005

Identification and functional characterization of a voltage-gated chloride channel and its novel splice variant in taste bud cells.

Taste bud cells are epithelial cells with neuronal properties. Voltage-dependent ion channels have been physiologically described in these cells. Here, we report the molecular identification and functional characterization of a voltage-gated chloride channel (ClC-4) and its novel splice variant (ClC-4A) from taste bud cells. ClC-4A skipped an exon near its 5'-end, incurring the loss of 60 amino acids at the N terminus. In situ hybridization and immunohistochemistry localized these two channels' transcripts and proteins to a subset of taste bud cells. Electrophysiological recordings of the heterologously expressed channels in Xenopus oocytes showed that ClC-4 and ClC-4A have opposite sensitivity to pH and unique ion selectivity. The chloride channel blockers niflumic acid and 5-nitro-2-(3-phenylpropylamino)benzoic acid had a slight or no inhibitory effect on the conductance of ClC-4, but both blockers inhibited ClC-4A, suggesting that ClC-4A is a candidate channel for an acid-induced 5-nitro-2-(3-phenylpropylamino)benzoic acid-sensitive current. Furthermore, these two channels may play a role in bitter-, sweet-, and umami-mediated taste transmission by regulating transmitter uptake into synaptic vesicles.

Alternative Splicing↗
PubMed2003

Spectrum of FANCA mutations in Italian Fanconi anemia patients: identification of six novel alleles and phenotypic characterization of the S858R variant.

Fanconi anemia (FA) is an autosomal recessive disorder characterized by genomic instability, bone marrow failure, congenital malformations, and cancer predisposition. FA is a genetically heterogeneous disease with at least seven genes so far identified. The role of FA proteins is unknown although they interact in a common functional pathway. Here, we report six novel FANCA sequence changes and review all the mutations identified in Italy. Except for two missense substitutions, all are expected to cause a premature termination of the FANCA protein at various sites throughout the molecule. The premature terminations are due to nonsense and splice site mutations, as well as small insertions and deletions, and large genomic rearrangements. The expected truncated proteins were not detectable on Western blot analyses. The FANCA-S858R variant is instead expressed at lower level than that seen in normal cell lines and is associated with a non-ubiquinated FANCD2 protein, strongly suggesting that the amino acid substitution is a disease-causing mutation. The spectrum of FA mutations is widely in agreement with the heterogeneous ethnic origin of the Italian population.

Alleles↗
PubMed1994

Generalized resistance to thyroid hormone: identification of a novel c-erbA beta thyroid hormone receptor variant (Leu450) in a Japanese family and analysis of its secondary structure by the Chou and Fasman method.

Generalized resistance to thyroid hormone (GRTH) is characterized by elevated circulating levels of thyroid hormone in the presence of a eumetabolic state and failure to respond to triiodothyronine. Various point mutations in the c-erbA beta thyroid hormone receptor gene are known to be responsible for different phenotypes of GRTH. We herein report a new c-erbA beta variant in a Japanese family. The variant consisting of a cytosine to adenine base substitution at nucleotide position 1650 altered phenylalanine to leucine in codon 450 in the T3-binding domain of c-erbA beta. This base substitution was found in one allele of the 2 affected members of the family. The in vitro translation products of this mutant c-erbA beta gene demonstrated a significantly reduced T3-binding affinity. The secondary structure of this mutant thyroid hormone receptor predicted by the Chou and Fasman method included a new turn in the alpha helix structure in the T3-binding domain. We also discuss the secondary structures of the previously reported mutant receptors.

Adolescent↗
PubMed1990

Identification and cDNA sequence of delta-preprotachykinin, a fourth splicing variant of the rat substance P precursor.

The neuropeptides substance P and neurokinin A are synthesised from a family of precursor polypeptides encoded by the preprotachykinin A (PPT) gene. In addition to a mRNA (beta-PPT) containing all 7 exons of the gene, alternatively spliced mRNAs lacking either exon 4 (gamma-PPT) or exon 6 (alpha-PPT) have been identified. We have determined the sequences of cDNA clones encoding four variants of PPT mRNA from rat dorsal root ganglion (DRG), including a novel mRNA species (delta-PPT) in which both exons 4 and 6 are absent. The sequence of delta-PPT predicts the existence of a novel tachykinin precursor polypeptide.

Amino Acid Sequence↗