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PubMed1988

A new transferrin variant from Iran (Tf B-Iran): review of 36 variant alleles.

A total of 2581 serum samples collected from five population groups of Iran was studied for electrophoretic variations of the transferrin (Tf). Besides the common phenotype Tf C the authors could observe 41 individuals with rare Tf types: CB1, CB2, CD1, CDChi, CD2. In addition to these Tf types two individuals with a new Tf B variant were observed. This new variant was found in the Dezfooli sample and was designated as Tf B-Iran. The electrophoretic position of this variant is described, and all the hitherto known Tf variants are reviewed.

Alleles↗

PubMed1980

Structure of a newly isolated variant of Simian virus 40 DNA containing monkey DNA and its similarity to previously isolated variants.

The structure of a newly and independently isolated defective variant of simian virus 40 that contains covalently linked monkey and SV40 DNA sequences is described. This variant, termed 290, has a structure essentially identical with a previously isolated and characterized variant named CVP8/1/P2 (Eco RI res). The structural similarities include the monkey (host) DNA segment that is combined with viral DNA sequences, the particular viral DNA segment that is present, and the arrangement of these within the defective genome. The monkey DNA segment contains sequences derived from both low and high reiteration frequency monkey DNA. The viral sequences include the origin of replication. The separate isolation of essentially identical variants suggests a high level of specificity in the events leading to the formation and amplification of this type of defective genome.

Animals↗

PubMed1988

Variant specific transcripts from the co-transposed segments of variant surface glycoprotein genes in Trypanosoma brucei.

We examined steady-state transcripts from the sequences immediately upstream of the 1 and 11 variant surface glycoprotein (VSG) genes in Trypanosoma brucei of the IsTaR 1 serodeme. These sequences, the co-transposed segment, differ in size and sequence, and produce a variety of variant-specific polyadenylated transcripts. Most, if not all, of these transcripts, some of which may be precursors, contain the spliced leader (SL). Variant specific transcription extends from 5' of the co-transposed segment to 100-400 nucleotides downstream of the major VSG mRNA polyadenylation site. The 1 VSG mRNA has at least 2, and possibly 3, SL addition sites; the major site is 120 nucleotides downstream of the polyadenylation site identified by sequencing a cDNA from the co-transposed segment. Two general models for the production of the co-transposed segment transcripts are discussed.

Animals↗

PubMed1982

Immunoglobulin V region variants in hybridoma cells. I. Isolation of a variant with altered idiotypic and antigen binding specificity.

The hybridoma cell line B1-8.delta 1 expresses an IgD antibody with specificity for the hapten 4-hydroxy-3-nitro-phenylacetyl (NP). Two monoclonal antibodies, each recognizing an idiotypic determinant (idiotope) in the variable region of antibody B1-8, and fluorescence-activated cell sorting were used for the isolation of spontaneous somatic cell variants whose antibody product lacks the expression of one of the two idiotopes. The variant cells carry a mutation which is expressed in the variable region of the antibody heavy chains and which reduces the affinity of the antibody for hapten greater than 100-fold. Idiotope loss variants of the selected phenotype are present in the B1-8.delta 1 cell population at low frequency.

Animals↗

PubMed1978

A preparative method for the isolation of genetic variant forms of glucosephosphate isomerase and a study of five variants.

A method has been developed for the rapid, quantitative separation of normal and abnormal glucosephosphate isomerase allozymes from individuals heterozygous for genetic variant forms of the enzyme. The method utilizes a substrate gradient elution of the enzyme from carboxymethyl Biogel and is far superior in terms of resolution and recovery to methods based on electrophoresis and isoelectric focusing. Five different genetic variant forms of the enzyme were isolated and subjected to a systematic comparison of their physical, catalytic and stability properties. While the physical and catalytic properties of most of the variants were similar, clear differences in the stability of the allozymes were apparent. In order to detect mutations affecting the stability, a series of different stability tests are required.

Genetic Variation↗

PubMed1978

An IgG2a-producing variant of an IgG2b-producing mouse myeloma cell line. Structural studies on the Fc region of parent and variant heavy chains.

The IgG2b-producing MPC 11 mouse myeloma cell line has yielded a number of variants which synthesize heavy chains characteristic of a different immunoglobulin subclass, IgG2a, as previously shown by serology, peptide maps, and assembly profiles. We have studied the Fc regions of the IgG2a protein synthesized by one variant, ICR 9.9.2.1, and of the IgG2b protein synthesized by MPC 11 and compared them to MOPC 173, an IgG2a protein of known sequence. We analyzed the Fc regions of the three immunoglobulins by several analytical techniques, such as immunoelectrophoresis of papain digests, NaDodSo4-polyacrylamide gel electrophoresis analyses of Fc CNBr fragments, and comparative ion-exchange chromatography of radiolabeled tryptic and chymotryptic Fc peptides. In addition, Fc CNBr fragments of the variant gamma2a and MPC 11 gamma2b molecules were isolated and subjected to amino acid analysis and partial sequence determination. From these data, we concluded that the Fc fragment of ICR 9.9.2.1 is most probably identical to that of MOPC 173 and different from the parental gamma2b Fc fragment. A number of residue positions which discriminate between gamma2b and gamma2a sequences are described. In two of three segments sequenced, gamma2b and gamma2a molecules share more identical residues than either shares with another mouse subclass, gamma1.

Amino Acid Sequence↗

PubMed1978

Isolation of myeloma variants with predefined variant surface immunoglobulin by cell sorting.

We describe a procedure for the isolation of somatic cell variants in which gene products are expressed on the cell surface that are not expressed in the wild type. Cloned cells of the myeloma line MPC 11, which expresses an IgG2b protein, were incubated with an antiserum specific for IgGI and IgG2a. Cells reacting with this antiserum were stained with a fluorescent anti-antiserum and enriched in three cycles of sorting in the fluorescence-activated cell sorter and subsequent growth in vitro. From the enriched population two variants were isolated by cloning in soft agar. One of them expressed a variant immunoglobulin that types serologically as an IgG2a but whose variable portion was idiotypically related to that of the MPC 11 wild-type protein.

B-Lymphocytes↗

PubMed1989

Nucleotide changes in sequential variants of influenza virus hemagglutinin genes and molecular structures of corresponding monoclonal antibodies specific for each variant.

We have generated four monoclonal antibodies specific for one or more members of a series of two sequentially derived PR8 influenza virus variants. Three of these antibodies share cross-reactive idiotypes. The amino acid sequences of these antibodies were determined, and it was found that two of these antibodies use genes from the VH7183 family, whereas the third uses a gene from the VHJ558 family. All four monoclonal antibodies derive from different families of genes encoding the variable region of the kappa chain. The RNA sequence of the parent PR8 virus as well as the RNA sequences of the sequential variants were also determined, and it was demonstrated that the variant hemagglutinin molecules differed from the parent molecule by only a single amino acid interchange. Despite these subtle differences in antigenic structures of hemagglutinin, and the cross-reactive idiotype of the antibodies, their primary structures were very different. These data reinforce the idea that a wide variety of antibody structures exist which are directed against subtly different structures in biologically important antigens.

Amino Acid Sequence↗

PubMed2026

Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.

Long-read sequencing enables improved detection of structural variants (SVs) in the human genome due to its substantially increased read lengths. However, currently widely used long-read SV callers primarily rely on alignment-based evidence, limiting their ability to detect large and complex SVs and potentially missing disease-relevant events. To address these limitations, we developed ContextSV, a framework that integrates alignment evidence with copy number predictions derived from sequencing coverage and single-nucleotide variant allele frequencies to improve SV detection, particularly for large copy number variants (CNVs). We additionally developed ContextScore, a machine learning-based classification model to assign SV confidence scores based on genomic context features and integrated it within ContextSV. Through benchmarking analyses on both simulated and real datasets, we demonstrate that ContextSV improves detection of large CNVs and inversions that may be missed by existing long-read SV callers. We further illustrate its utility by identifying and experimentally validating multiple large SVs in the KOLF2.1J reference stem cell line that were not detected by other methods. Collectively, our results demonstrate that ContextSV serves as a valuable complement to existing long-read SV detection approaches by improving sensitivity for large and clinically relevant SVs.

Humans↗

PubMed1989

Purification and characterization of five variants of phospholipase A2 and complete primary structure of the main phospholipase A2 variant in Heloderma suspectum (Gila monster) venom.

1. Five increasingly anionic variants (Pa1-Pa5) of Ca2+-dependent phospholipase A2 were purified to homogeneity from the venom of the lizard Heloderma suspectum (Gila monster). The purification procedure was based on semi-preparative reverse-phase HPLC followed by anion-exchange HPLC and analytical reverse-phase HPLC. 2. Their Mr were 17,000-18,000, as deduced by SDS/PAGE. Specific activities tested by the capacity to hydrolyze phosphatidylcholines at pH 8.5 decreased as follows: Pa3 greater than Pa5 greater than Pa4 greater than Pa1 greater than Pa2. These activities showed the same optimum pH (9.0), were mainly of the phospholipase A2 type and were lost upon p-bromophenacyl bromide treatment. 3. All five phospholipases efficiently stimulated amylase release from dispersed rat pancreatic acini at pH 7.4, their potency decreasing as follows: Pa2 greater than Pa1 approximately equal to Pa4 greater than Pa3 approximately equal to Pa5. No deleterious effect was apparent based on the lack of lactate dehydrogenase release. 4. The five variants, Pa1-Pa5, differed significantly in amino acid composition and this, together with distinct antigenic properties of Pa2 and Pa5, establishes the subheterogeneity of this new type of phospholipase A2, despite the fact that the N-terminal amino acid sequence (31 residues) of Pa1-Pa5 was exactly the same. 5. The full sequence of the major variant, Pa5, showed that this 142-amino-acid protein exhibited greater similarity to the bee venom enzyme than to any class I or class II secretory phospholipase A2 from snake venom and mammalian pancreas. While Pa5 displayed the highly conserved region between Asp30 and Cys39 (the essential active site of all phospholipases A2), its salient original points included 10 half-cystine residues only, an incomplete N-terminal sequence, large changes in the putative calcium loop, several alterations after the active site and a C-terminal extension never seen in other phospholipases A2, with the only exception being bee venom.

Amino Acid Sequence↗

PubMed1991

Isolation of chick tenascin variants and fragments. A C-terminal heparin-binding fragment produced by cleavage of the extra domain from the largest subunit splicing variant.

The extracellular-matrix glycoprotein, tenascin, consists of disulfide-linked subunits of 190, 200 and 230 kDa (the three splicing variants reported in chicken) and usually exists as a six-armed structure under the electron microscope. We used monoclonal antibodies to isolate and characterize different splicing variants and proteolytic fragments obtained from the native protein. Purified monomeric tenascin has a native molecular mass of 216 kDa and is structured as single arms. Tenascin fragments obtained by pepsin digestion bind to monoclonal antibody (mAb) TnM1 which is directed against epidermal-growth-factor-like repeats in the N-terminal half of all subunits. These fragments represent the thin proximal part of the tenascin arms and they are still partially linked to dimers and trimers via disulfide bridges. Using mAb Tn68, that reacts with a fibronectin-type-III repeat towards the C-terminus, a tenascin fragment, generated by treatment with pronase, can be isolated. Ultrastructurally, this fragment looks like the thicker distal part of the tenascin arms. Only the 230-kDa variant of tenascin gives rise to this distal fragment after cleavage within the alternatively spliced fibronectin-type-III repeats. Native tenascin and all fragments containing the distal part of its arms bind to heparin-agarose, whereas the proximal fragments do not. Oligomeric and monomeric tenascin inhibit fibronectin-mediated fibroblast spreading with comparable efficiency when added to the culture medium, while the proximal fragment has no effect. The distal fragment as well as reduced and alkylated tenascin are active in this assay, but only at higher molar concentrations when compared to the native protein.

Animals↗

PubMed1976

Distribution of G6PD types in the population of southwest France: common variants and new variants.

Glucose-6-phosphate dehydrogenase was purified from blood samples originating from 33 subjects living in the 'Midi-Pyrenees' region (Southwest France). Biochemical and electrophoretic characteristics of several enzymatic variants were revealed. The distribution of the mutations in the subjects studied gave the following results: (1) Meditteranean Gd(-) and Gd(-)A identified variants; they constitute the main part of our observations. (2) Two original variants confirmed by the WHO International Reference Laboratory, that is: Gd(-) Toulouse and Gd(+) Luz-Saint-Sauveur; the latter mutation did not produce any haematological disorder. Absence of chronic haemolytic anaemia as well as a high rate of favism could be found in the families studied. As it is generally observed in Mediterranean regions, Southwest France population is characterized by a certain heterogeneity in biochemical and genetic mutations.

Erythrocytes↗

PubMed1985

Some anatomical variants and pitfalls in computed tomography of the trachea and mainstem bronchi. II. Compression or anatomical variants?

472 computed tomographic (CT) examinations in 448 patients were reviewed for depression of the wall of the trachea and mainstem bronchi. Depression was defined as a neutral term, not indicating pressure exerted upon the wall. Such depressions appeared to occur very frequently as a variant. Special attention is paid to the so-called azygos vein indentation. The most marked depression variants in our series are reproduced. When a depression is found in contiguity with a pathological mass and does not exceed the range of the variants, one cannot be sure that the mass is indeed the cause of this depression. In patients with bronchogenic carcinoma, depression of the wall of the trachea or mainstem bronchus seems to be no better sign for the metastatic nature of lymphadenopathy than size per se.

Azygos Vein↗

PubMed1988

Stable variant-specific transcripts of the variant cell surface glycoprotein gene 1.8 expression site in Trypanosoma brucei.

The structure and transcriptional regulation of the 1.8 variant cell surface glycoprotein (VSG) gene expression site located on a 430-kilobase (kb) chromosome was examined in a 430-kb-chromosome-specific library. Using 32P-labeled nascent transcripts generated by nuclear run-on, we selected recombinant clones derived from the 430-kb chromosome which were coordinately activated with the 1.8 VSG gene. The results show that a repetitive region with a minimum size of 27 kb is coordinately activated with the 1.8 VSG gene. As with the 1.8 VSG gene, transcription is by RNA polymerases that are insensitive to the drug alpha-amanitin at concentrations up to 1 mg/ml. Transcription results in the generation of several stable variant-specific mRNAs. These mRNAs most likely belong to a family of repetitive expression-site-associated genes.

Animals↗

PubMed1989

Role of variant prealbumin in the pathogenesis of familial amyloidotic polyneuropathy: fate of normal and variant prealbumin in the circulation.

According to recent studies on protein chemistry and genetic engineering, replacement of the Val30 residue of prealbumin by methionine is believed to play a critical role in the formation of amyloid deposit and the pathogenesis of familial amyloidotic polyneuropathy (FAP). However, only limited information is available concerning the behavior of prealbumin in the circulation. To obtain the molecular insight into the mechanism of amyloid deposition, it is indispensable to know the fates of normal and variant prealbumin in vivo. Thus, the fates of prealbumin samples from normal and FAP patients were studied in normal rats as well as in animals that were challenged with acute inflammation induced by turpentine. The effect of in vitro photooxidation of prealbumin samples on their behavior was also examined in vivo. Kinetic analysis revealed no appreciable difference between prealbumin samples from normal and FAP patients. These results suggest that factors other than the rate of transfer of the variant form prealbumin from plasma to an extravascular compartment may play a critical role in the pathogenesis of amyloid deposition in FAP patients.

Amyloidosis↗

PubMed1989

Testis-specific histone H1t is truly a testis-specific variant and not a meiotic-specific variant.

Immunoblotting studies using highly specific polyclonal anti-histone H1t-IgG, which was extensively characterized by us previously, did not produce a signal with any of the histone H1 subtypes of either 1-day-old or adult rat ovarian nuclei. The absence of histone H1t in ovarian nuclei was also confirmed by indirect immunofluorescence studies. It is concluded, therefore, that histone H1t is truly a testis-specific histone variant and not a meiotic-specific variant.

Animals↗

PubMed1989

Comparison of partial amino acid sequences of two protamine 2 variants from stallion sperm. Structural evidence that the variants are products of different genes.

Protamine 1 and two protamine 2 variants were isolated from stallion sperm and separated by acetic acid-urea gel electrophoresis. After electroblotting onto polyvinyldifluoride filters, their amino-terminal amino acid sequences were determined by pulse-liquid peptide sequencing. The sequences of the two protamine 2 variants are homologous but slightly different in length and amino acid composition and indicate for the first time the existence of two different genes for this protamine species.

Amino Acid Sequence↗

PubMed1990

VARIANT: a store and retrieval system for human haemoglobin variants.

VARIANT, a FORTRAN 77 computer system for storing and retrieving the amino acid replacements in human haemoglobin variants on a multicriterion basis, is presented. The system is transportable and user-friendly, can easily be expanded and can also be used to create a database of the amino acid replacements in families of homologous proteins, becoming an efficient tool for evolutionary studies.

Amino Acids↗