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PubMed1990

C2 reference typing report.

Thirty samples contributed by seven laboratories to the VIth Complement Genetics Workshop were analyzed by isoelectric focusing and immunoblotting with a specific antihuman C2 antibody for the study of the polymorphism of native, activated and desialated C2. This study allowed to compare almost all the C2 variants so far described and also several 'new variants'. According to our results, the C2 system consists of nine structural variants at the protein level which include the common C2 C, the less common C2 B (in Caucasoids), four rare acidic and three rare basic variants. The polymorphic site for the basic variants is carried by the C2a fragment. Typing of desialated C2 is necessary to identify rare acidic or basic variants, especially the C2 BH and C2 BJ variants which seem difficult to be recognized in the native protein.

Antibodies↗
PubMed1994

Electrophoretic screening for genetic variation in apolipoprotein C-III: identification of a novel apoC-III variant, apoC-III(Asp45-->Asn), in a Turkish patient.

Screening of 6,840 plasma samples by isoelectric focusing (IEF) led to the identification of a novel apolipoprotein C-III variant. The underlying molecular defect was established by sequencing of exons 3 and 4 of the apoC-III gene subsequent to their amplification by the polymerase chain reaction (PCR). A G-->A transition in the first nucleotide of codon 45 results in a replacement of aspartic acid by asparagine. ApoC-III(Asp45-->Asn) was detected in a Turkish patient who previously had undergone coronary bypass surgery. Family studies identified two of the three children of the index patient as heterozygous variant carriers. The family was too small to demonstrate a significant effect of the variant on lipid metabolism. However, as judged by two-dimensional immunoelectrophoresis as well as IEF and subsequent scanning densitometry, the concentrations of the variant allele products were increased twofold in very low density lipoproteins (VLDL) and slightly decreased both in low density lipoproteins (LDL) and in high density lipoproteins (HDL) relative to the concentrations of the normal allele products. The disproportional distribution of the variant apoC-III isoproteins may indicate differences in the metabolism of variant and normal apoC-III. We conclude that genetically determined structural variants of apoC-III with changes in complete net charges are very rare and, hence, do not significantly contribute to the formation of dyslipidemia in the German population. Although heterozygosity for apoC-III(Asp45-->Asn) is not associated with severe dyslipidemia, the disproportional distribution of the allele products among plasma lipoproteins indirectly indicates some impact on lipoprotein metabolism.

Alleles↗
PubMed1983

Immunological detection of the sixth complement component (C6) following flat bed polyacrylamide gel isoelectric focusing and electrophoretic transfer to nitrocellulose filters.

A method for the electrophoretic transfer of C6 molecules to a nitrocellulose filter is described. The protein is detected by the use of anti-C6 antibodies and a peroxidase conjugated antibody. Using this method typical isoelectric patterns of C6 variant phenotypes are found. Inheritance and population data are presented. Three rare structural variants, one of which appears to be previously unreported, were discovered among a sample of 202 individuals. The method is discussed from the viewpoint of its flexibility and its value as an additional tool for revealing inherited variations in structural gene products.

Antibodies↗
PubMed1989

Structural analysis of the HLA-DR, -DQ, and -DP alleles on the celiac disease-associated HLA-DR3 (DRw17) haplotype.

Celiac disease is strongly associated with the HLA class II D-region serologic markers DR3 (DRw17) and DQw2. Moreover, by restriction fragment length polymorphism analysis, greater than 90% of DR3 (DRw17), DQw2 celiac disease patients have a polymorphic 4.0-kilobase Rsa I DP B gene DNA fragment. The present study sought to determine if there is a unique HLA class II D-region A or B gene structural variant on the DR3 (DRw17) haplotype found in celiac disease. The polymorphic second exons of the coding DRB, DQA and DQB, and DPA and DPB genes in celiac disease patients with the DR3 (DRw17) haplotype were sequenced after amplification by the polymerase chain reaction. To define the DP B genes associated with celiac disease, the second exons of the coding DP B genes from 27 celiac disease patients were amplified similarly and probed by using a panel of sequence specific oligonucleotides. The HLA-DR, -DQ, and -DP A and B gene second exon sequences of celiac disease patients were noted to be identical to sequences that can be found also, although at a significantly lower frequency, in unaffected individuals. This is compatible with a disease model wherein the HLA class II genes on the DR3 (DRw17) haplotype are necessary, but not sufficient, for the phenotypic expression of celiac disease. Analysis of the DP B genes revealed a significant increase in the frequency of the alleles DPB1 and DPB3 in celiac disease. Furthermore, the increased frequency of the 4.0-kilobase Rsa I DP B gene restriction fragment length polymorphism in celiac disease can be accounted for by the overrepresentation in disease of the alleles DPB1 and DPB3. The HLA-associated susceptibility to celiac disease appears to be multigenic, with specific, but structurally normal, allelic variants in the DP and DQ/DR subregions contributing to disease susceptibility.

Alleles↗
PubMed1982

[Chinese hamster cells with mutation in the hypoxanthine-guanine phosphoribosyltransferase locus. III. The biochemical characteristics of the hypoxanthine-guanine phosphoribosyltransferase of complementing mutants].

The paper presents a biochemical study of hypoxanthine-guanine phosphoribozyltransferase (HRPT) in mutant clones of Chinese hamster cells showing an ability for complementation. In order to characterize HPRT, its kinetic properties, temperature sensitivity and electrophoretic mobility in polyacrylamide gel were assayed. According to the complementation map, the nine mutant clones studied can be divided into four complementation groups. All these clones have been shown to be mutants with respect to the HPRT structural gene, as they synthesize the structurally and functionally altered enzyme. A comparative biochemical analysis of HPRT in the four complementation groups revealed substantial differences in mutant enzymes from different groups; hence, the possibility of complementation on the molecular level. All biochemical characteristics of HPRT tested are similar in clones belonging to one and the same complementation group, which could indicate that they have the same structural variant of the enzyme, regardless of the manner in which the mutants were obtained. Having revealed the similarity and the distinctive features of mutant enzymes within complementation groups, the biochemical analysis confirmed the results of complementation analysis and added the structural information concerning mutant variants of the enzyme. Thus, the complementation map of the HPRT gene yielded by hybridological analysis has been tested and confirmed by an independent biochemical study. Complementation analysis applied to the HPRT mutants made it possible to identify qualitatively distinct groups. Each of these groups may be regarded as an allele of the gene, and the sum of the groups may be regarded as a series of multiple alleles.

Animals↗
PubMed1979

Isolation and characterization of the histone variants in chicken erythrocytes.

Chicken erythrocyte histones 2A, 2B, and 3 can be resolved into nonallelic primary structure variants by polyacrylamide gel electrophoresis in the presence of Triton X-100. These variants were isolated and characterized by analysis of their tryptic and thermolytic peptides. The major variants of chicken H2A and H2B differ from the analogous component of calf thymus by a small number of conservative amino acid substitutions in the basic terminal regions, which interact with DNA. This moderate rate of allelic evolution of the slightly lysine-rich histones contrasts with the complete conservatism found in the arginine-rich histones. Chicken H4 and both chicken H3 variants are identical with their corresponding components in mammals. The amino acid substitutions distinguishing histone variants are located within the highly conserved hydrophobic regions, which are involved in histone--histone interactions.

Amino Acids↗
PubMed1992

The mouse plasminogen locus maps to the recombination breakpoints of the tLub2 and TtOrl partial t haplotypes but is not at the tw73 locus.

The mouse plasminogen (Plg) locus maps to a region of chromosome (Chr) 17 which is inverted in the t haplotype Chromosomal variant. Here we investigate the genomic organization of the Plg locus in structurally variant forms of Chr 17; wild-type (+), t haplotype (t), and two partial t haplotypes TtOrl and tLub2 which arose by recombination between + and t chromosomes. Our analysis suggests that the t haplotype chromosomal variant contains extra, inverted copies of the Plg locus, and that a single locus is present in the wild-type variant. Changes in the Plg locus in TtOrl and tLub2 suggest that they arose by homologous recombination across elements in the Plg locus having the same orientation in the wild-type and t haplotype chromosomes. One hundred ten kb around the wild-type Plg genomic locus have been cloned and the proximal breakpoint of a deletion in the tLub2 chromosome has been localized to a fragment 30 kb downstream of the Plg gene. The tLub2 deletion has been shown to delete a gene named tw73 that affects blastocyst implantation, a process probably requiring proteases such as plasminogen. However, the mapping of Plg relative to the tLub2 deletion and mRNA analysis of plasminogen in tw73 heterozygotes suggests that Plg does not lie at the tw73 locus.

Animals↗
PubMed1989

Synthesis and evaluation of some new retinoids for cancer chemoprevention.

Many derivatives and analogs of the natural vitamin A compounds have been synthesized, and some of these retinoids are very active in various bioassays that may be predictive for cancer chemopreventive activity. Analogs have been synthesized in which parts of one, or more, of the three traditional subdivisions of the retinoid structure--the terminal polar group, the conjugated side chain, and the cyclohexenyl region--have been altered or replaced. In addition, structural alterations have produced compounds (arotinoids) in which two, or more, aromatic rings replace much of the classical retinoid structure. Further structural modifications that effected replacement of the entire retinoid structure by aromatic groups and certain linking groups have been made. Some of the arotinoids and further structural variants, which appear superficially to represent immense alteration of the classical retinoid structure, have potent activity in various retinoid bioassays. Four types of new classical retinoids (retinoylamino acids, bifunctional analogs, retinyl ethers, and 4-oxoretinoid derivatives) have been synthesized and evaluated in our laboratories. All-trans- and 13-cis-retinoyl alpha-amino acids are active in a hamster trachea organ culture assay and show much promise in potentiating immune responses. Retinoic acid analogs that have a bifunctional terminus bind to CRABP even though they have a bulky alpha-substituent, induce differentiation of F9 embryonal carcinoma cells, and have good activity in an immune-potentiation assay. A new retinyl either, retinyl propynyl ether, has chemopreventive activity against mammary carcinogenesis in vivo. Oral administration of this retinoid produces high and sustained concentrations in the rat mammary gland. New congeners of 4-oxoretinoic acid demonstrate high activity in a spectrum of bioassays.

Animals↗
PubMed1981

cis-Interacting genes in the S region of the murine major histocompatibility complex.

Insight into the control of gene expression may be gained by analysing genetic systems marked by both regulatory and structural variants. In such systems one can determine whether a regulatory element controls structural genes on both chromosomes or only on the chromosome to which it is linked. The latter may be detected in individuals heterozygous at both the regulatory and structural loci, in which case the effect of each regulatory allele is seen to be exerted only on the cis-located structural allele. In prokaryotic organisms, the identification of cis interaction of this sort has allowed elucidation of many features of genetic regulation, first for the lac operon and subsequently for a variety of other systems. In higher organisms, however, there have been few opportunities to observe cis-interacting genes. The most thoroughly characterized mammalian system in this regard is the murine beta-glucuronidase locus described by Paigen and his colleagues, in which cis interaction has been shown to occur between two closely linked genetic elements-the beta-glucuronidase structural gene itself and an androgen-activated regulatory gene which controls the quantity of beta-glucuronidase expressed. We report here that cis-interacting genetic elements are also found in the S region of the mouse major histocompatibility complex H-2.

Animals↗
PubMed2005

Growth of silicon nanowires on H-terminated Si {111} surface templates studied by transmission electron microscopy.

We have studied the growth of silicon nanowires (SiNWs) by means of transmission electron microscopy. SiNWs are grown from nanocatalysts via the Vapor-Liquid-Solid (VLS) mechanism using silane (SiH4) gas as a source gas. The nanocatalysts are prepared on a hydrogen (H)-terminated Si surface. We have examined the formation mechanism of nanocatalysts on H-terminated surface and have observed several structural variants of SiNWs. According to the study we have suggested that many structural variations of SiNWs are possible, which modify the structural properties of SiNWs to great extents.

Journal Article↗
PubMed2025

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species.

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

Quercus↗
PubMed2000

Growth hormone size variants: changes in the pituitary during development of the chicken.

There is considerable evidence for the existence of structural variants of growth hormone (GH). The chicken is a useful model for investigating GH heterogeneity as both size and charge immunoreactive-(ir) variants have been observed in the pituitary and plasma. The present study examined the size distribution of ir-GH in the pituitary gland of chicken, from late embryogenesis through adulthood. Pituitaries were homogenized in the presence of protease inhibitor, and the GH size variants were separated by SDS-PAGE, transferred by Western blotting, immunostained with a specific antiserum to chicken GH, and quantitated by chemiluminescence followed by laser densitometry (chemiluminescent assay). Under nonreducing conditions ir-GH bands of 15, 22, 25, 44, 50, 66, 80, 98, 105 and >110 kDa were observed. Both the relative proportion of the GH size variants and the total pituitary content varied with developmental stage and age. The proportion of the 15-kDa fragment was greatest in the embryonic stage, and then it decreased. The proportion of the monomeric 22-kDa form was lowest at 18 days of embryogenesis (dE) and highest at 20 dE. In contrast, the high MW forms (>/=66 kDa) were lowest in embryos, and they increased (P < 0.05) after hatching. The 22-, 44-, 66-, and 80-kDa forms were assayed for activity by radioreceptor assay following isolation by semipreparative SDS-PAGE. Only the 22-kDa GH variant showed radioreceptor activity. Under reducing conditions for SDS-PAGE, ir-GH bands of 13, 15, 18, 23, 26, 36, 39, 44, 48, 59 and 72 kDa were oberved, but most of the high MW form disappeared. There was a concomitant increase in the proportion of the monomeric band and of several submonomeric forms. The present data indicate that the expression, processing, and/or release of some if not all size variants are under some differential control during growth and development of the chicken.

Aging↗
PubMed1997

Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes.

A dynamical model of interdomain "hinge bending" of T4 lysozyme in aqueous solution has been developed on the basis of molecular dynamics (MD) simulation. The MD model study provides a description of the conformational reorganization expected to occur for the protein in aqueous solution as compared to the crystalline environment. Three different 500 ps molecular dynamics simulations were calculated, each using a distinctly different crystal conformation of T4 lysozyme as the starting points of the MD simulations. Crystal structures of wild-type lysozyme and "open" and "closed" forms of M61 variant structures were analyzed in this study. Large-scale, molecular-conformational rearrangements were observed in all three simulations, and the largest structural change was found for the open form of the M61 allomorph. All three simulated proteins had closed relative to the wild-type crystal structure, and the closure of the "jaws" of the active site cleft occurred gradually over the time course of the trajectories. The time average MD structures, calculated over the final 50 ps of each trajectory, had all adapted to conformations more similar to each other than to their incipient crystal forms. Using a similar MD protocol on cytochrome P450BM-3 [M. D. Paulsen and R. L. Ornstein (1995) Proteins: Structure Function and Genetics, Vol. 27, pp. 237-243] we have found that the opposite type of motion relative to the starting crystal structure, that is, the open form of the crystal structure, had opened to a greater degree relative to the incipient crystal structure form. Therefore we do not believe that either result is merely a simulation artifact, but rather the protein dynamics are due to protein relaxation in the absence of crystal packing forces in the simulated solution environments.

Bacteriophage T4↗
PubMed2004

The structure of the carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-79104.

The structure of the carbohydrate backbone of the lipopolysaccharide from Pectinatus frisingensis strain VTT E-79104 was analyzed using chemical degradations, NMR spectroscopy, mass spectrometry, and chemical methods. The LPS contains two major structural variants, differing in the presence or absence of an octasaccharide fragment. The largest structure of the carbohydrate backbone of the LPS, that could be deduced from experimental results, consists of 20 monosaccharides arranged in a nonrepetitive sequence: [carbohydrate structure: see text] where R is H or 4-O-Me-alpha-L-Fuc-(1-2)-4-O-Me-beta-Hep-(1-3)-alpha-GlcNAc-(1-2)-beta-Man-(1-3)-beta-ManNAc-(1-4)-alpha-Gal-(1-4)-beta-Hep-(1-3)-beta-GalNAc-(1- where Hep is a residue of D-glycero-D-galacto-heptose; all monosaccharides have the D-configuration except for 4-O-Me-L-Fuc and L-Ara4N. This structure is architecturally similar to the oligosaccharide system reported previously in P. frisingensis VTT E-82164 LPS, but differs from the latter in composition and also in the size of the outer region.

Acetylation↗
PubMed1999

Emergence of Anaplasma marginale antigenic variants during persistent rickettsemia.

Anaplasma marginale is an ehrlichial pathogen of cattle, in the order Rickettsiales, that establishes persistent cyclic rickettsemia in the infected host. Within each rickettsemic cycle, A. marginale expressing antigenically variant major surface protein 2 (MSP2) emerge. By cloning 17 full-length msp2 transcripts expressed during cyclic rickettsemia, we determined that emergent variants have a single, central hypervariable region encoding variant B-cell epitopes. The N- and C-terminal regions are highly conserved among the expressed A. marginale variants, and similar sequences define the MSP2 homologues in the agent of human granulocytic ehrlichiosis (HGE). This is in contrast to the MSP2 homologues in ehrlichial genogroup I pathogens, Ehrlichia chaffeensis, Ehrlichia canis, and Cowdria ruminantium, that have multiple hypervariable regions. By defining the variable and conserved regions, we were able to show that the single hypervariable region of A. marginale MSP2 encodes epitopes that are immunogenic and induce variant-specific antibody responses during persistent infection. These findings demonstrate that the MSP2 structural variants that emerge during each cycle of persistent rickettsemia are true antigenic variants, consistent with MSP2 antigenic variation as a mechanism of A. marginale persistence.

Amino Acid Sequence↗
PubMed1984

Polyomavirus growth and persistence in Friend erythroleukemic cells.

Infection of Friend erythroleukemic (FL) cells by polyomavirus (Py) invariably results in the selection of persistently infected FL-Py cell lines and clones. Anti-Py serum treatment of FL-Py lines and clones leads to the loss of Py genome and consequent cell cure. Conversely, cure has not been obtained in FL-PytsA cell lines (isolated after infection by a Py thermosensitive early mutant) and their derivative clones cultivated for a long time at nonpermissive temperature (39 degrees C), where viral large-T protein is inactive. Rescue of viral particles has always been obtained after shifting cells to 32 degrees C. Integrated viral genomes were detected by blot hybridization in an FL-PytsA clone at 39 degrees C. Long-term observation of FL-Py cell lines and their derivative clones reveals a reciprocal selection mechanism (coevolution) between the viral and the cellular populations, resulting in either a completely virus-free Py-resistant FL cell line (cure) or in a continuously Py-shedding line bearing Py genome variants. Structural analysis of these viral populations has been carried out, and some viral variants have been isolated and characterized. On the basis of the results obtained, the possible mechanisms of Py persistence in FL cells will be discussed.

Animals↗
PubMed1988

The central projections of the stretch receptor neurons of crayfish: structure, variation, and postembryonic growth.

Each stretch receptor neuron (SR) of the crayfish abdomen projects from its peripherally located soma an axon that enters the CNS through the second nerve (N2) of its segmental ganglion. Co2+ backfills of N2 revealed that this axon bifurcates, sending one branch to the brain and the other to the terminal abdominal ganglion. Each axon makes many short lateral branches as it traverses each of the other segmental ganglia, and has 2 major arborizations--one in the tritocerebrum of the brain and the other in the terminal abdominal ganglion, G6. These projections to G6 are described in detail. Individual SR axons from different segments were impaled in G6 with a Lucifer yellow-filled microelectrode, identified physiologically, and then filled to discover their structures. In a sample of more than 50 SR neurons, no systematic structural differences between the projections of phasic SR neurons and tonic SR neurons were observed. Three kinds of structural variability occurred in these projections to G6: unusual primary axon shape, long primary axon, and large terminal varicosities. Comparisons of SR neurons that originated in different segments revealed a segmental gradient in the probability of each structural variant. SR neurons from more anterior segments were more likely to show these structural variations. Comparisons of these variations in crayfish of different sizes showed that unusual primary axon shape and long primary axons were more probable in large crayfish than in small ones. Therefore, these variations are probably the products of postembryonic growth of the nervous system.

Animals↗
PubMed1982

The primary structure of genetic variants of mouse hemoglobin.

The primary structures of the alpha globins from CE/J, DBA/2J, and a stock of Potter's mice were determined to identify the amino acid substitutions associated with the unique isoelectric focusing patterns of these hemoglobins. In addition, the primary structures of the alpha globins from MOL III and PERU mice were studied in search of amino acid substitutions that may not be detected by isoelectric focusing. CE/J hemoglobin contains a unique kind of alpha globin called chain 5. It differs from the single kind of alpha globin (chain 1) in C57BL/6 by having alanine rather than glycine at position 78. DBA/2J hemoglobin has two kinds of alpha globins: one half is like chain 5 and the other half is like chain 1. The hemoglobin from Potter's stock of Mus musculus molossinus also contains chains 1 and 5, but they are expressed at different levels i.e., 80% chain 1 and 20% chain 5. MOL III hemoglobin has a single kind of a alpha globin identical to that in C57BL/6, and PERU hemoglobin contains approximately 40% chain 1 and 60% chain 4. Chains 1 and 4 have different amino acids at positions 25, 62 and 68. These studies confirm that mouse hemoglobins separable by isoelectric focusing, but not by other means of electrophoresis, have substitutions of neutrally charged amino acids in their alpha chains.

Amino Acid Sequence↗