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PubMed1981

Structural variation among human beta-tubulin genes.

A chicken beta-tubulin cDNA probe has been used to screen two independently generated human genomic libraries. Of 13 EcoRI fragments detectable in a human genomic Southern blot experiment, 7 correspond in size to EcoRI fragments isolated from recombinant bacteriophage. The location of beta-tubulin-specific regions and the direction of transcription were determined within each cloned fragment. One clone (5 beta) contained a beta-tubulin-specific region of 6.8 kilobase pairs (kbp) that included three intervening sequences as well as a number of inverted repeat structures. The remaining clones contained beta-tubulin-specific sequences that were close to or, in two cases, substantially less than 1.9 kbp long. Because mature human beta-tubulin mRNA is approximately 1.9 kbp long, these short DNA regions cannot on their own encode a functional beta-tubulin mRNA. Analysis using 3'- and 5'-specific probes derived from the chicken cDNA clone showed the presence of both of these end regions within one truncated tubulin-like sequence. A second short tubulin-specific region failed to hybridize with a 3'-specific probe. These short sequences are therefore likely to be examples of pseudogenes that have arisen by loss of a portion of DNA essential to the production of functional human beta-tubulin mRNA.

Animals↗
PubMed1981

Fetal lung hypoplasia: biochemical and structural variations and their possible significance.

Quantitative biochemical criteria for lung growth and maturation were compared with the histological appearances in hypoplastic lungs from 20 fetuses and newborn infants. Cases associated with oligohydramnios showed a characteristic series of changes with narrow airways, retardation of epithelial and interstitial growth, delay in development of blood-air barriers, and low concentrations of phospholipid phosphorus, lecithin phosphorus, total palmitate, and lecithin palmitate. The growth and maturation arrest appeared to affect the peripheral part of the acinus. Examples of other types of lung hypoplasia showed different features. Hypoplastic lungs from infants with normal or increased amniotic fluid were of mature structure with phospholipid concentrations similar to those of infants with normally developed lungs at term. The hypoplastic left lung in 2 cases of congenital diaphragmatic hernia had an immature structure with low phospholipid concentrations, whereas the right lung has structurally and biochemically more mature. It is suggested that fetal lung growth may be impaired by any influence which reduces thoracic volume but that maturation arrest is due specifically to loss of the ability to retain lung liquid.

DNA↗
PubMed1993

Conformational structure variations in DNA: a PCILO study.

Perturbative configuration interaction using localized orbital (PCILO) computations have been carried out on conformational preference of d(GpC) and d(CpG) units of Z-II DNA. By keeping the sugar pucker fixed in the crystallographic conformation, PCILO energies have been calculated as a function of torsion angles alpha and zeta around two P-O ester bonds with preselected values of beta, gamma and epsilon. The results indicate that the d(GpC) unit is energetically more stable than the d(CpG) unit and prefers a g+ t conformation in (alpha-zeta) hyper-space observed in the crystal structure. The d(CpG) unit, on the other hand, shows intrinsic preference for g-g- conformation with other torsion angles close to DNA-B structure. The possibility of d(GpC) unit responsible for the stability of Z-helix has been discussed.

Base Sequence↗
PubMed2000

Structural variation in the 16S-23S rRNA intergenic spacers of Vibrio parahaemolyticus.

The 16S-23S rRNA intergenic spacers (IGS) of Vibrio parahaemolyticus were PCR-amplified and cloned with pT7Blue T vector. A total of six clones were isolated dependent on size difference. The clones were different with respect to both the number and the composition of the tRNA genes included, and were designated IGS-0, IGS-E, IGS-IA, IGS-AE, IGS-EKV and IGS-EKAV. IGS-EKAV included the cluster of tRNA(Glu)-tRNA(Lys)-tRNA(Ala)-tRNA(Val); IGS-EKV, tRNA(Glu)-tRNA(Lys)-tRNA(Val); IGS-AE, tRNA(Ala)-tRNA(Glu); IGS-IA, tRNA(Ile)-tRNA(Ala); and IGS-E, tRNA(Glu). IGS-0 had no tRNA gene. Some similarities were found in the nucleotide sequence of the non-coding regions flanked by the tRNA genes. The structure difference found in the spacers is meaningful for elucidating the evolutionary line of each ribosomal RNA operon and the profile is applicable as a molecular marker of the bacterium.

Cloning, Molecular↗
PubMed2005

The R1 resistance gene cluster contains three groups of independently evolving, type I R1 homologues and shows substantial structural variation among haplotypes of Solanum demissum.

Cultivated and wild potatoes contain a major disease-resistance cluster on the short arm of chromosome V, including the R1 resistance (R) gene against potato late blight. To explore the functional and evolutionary significance of clustering in the generation of novel disease-resistance genes, we constructed three approximately 1 Mb physical maps in the R1 gene region, one for each of the three genomes (haplotypes) of allohexaploid Solanum demissum, the wild potato progenitor of the R1 locus. Totals of 691, 919 and 559 kb were sequenced for each haplotype, and three distinct resistance-gene families were identified, one homologous to the potato R1 gene and two others homologous to either the Prf or the Bs4 R-gene of tomato. The regions with R1 homologues are highly divergent among the three haplotypes, in contrast to the conserved flanking non-resistance gene regions. The R1 locus shows dramatic variation in overall length and R1 homologue number among the three haplotypes. Sequence comparisons of the R1 homologues show that they form three distinct clades in a distance tree. Frequent sequence exchanges were detected among R1 homologues within each clade, but not among those in different clades. These frequent sequence exchanges homogenized the intron sequences of homologues within each clade, but did not homogenize the coding sequences. Our results suggest that the R1 homologues represent three independent groups of fast-evolving type I resistance genes, characterized by chimeric structures resulting from frequent sequence exchanges among group members. Such genes were first identified among clustered RGC2 genes in lettuce, where they were distinguished from slow-evolving type II R-genes. Our findings at the R1 locus in S. demissum may indicate that a common or similar mechanism underlies the previously reported differentiation of type I and type II R-genes and the differentiation of type I R-genes into distinct groups, identified here.

Chromosomes, Artificial, Bacterial↗
PubMed2006

Evolution of the primate cathelicidin. Correlation between structural variations and antimicrobial activity.

Cathelicidin genes homologous to the human CAMP gene, coding for the host defense peptide LL-37, have been sequenced and analyzed in 20 primate species, including Great Apes, hylobatidae, cercopithecidae, callithricidae, and cebidae. The region corresponding to the putative mature antimicrobial peptide is subject to a strong selective pressure for variation, with evidence for positive selection throughout the phylogenetic tree relating the peptides, which favors alterations in the charge while little affecting overall hydrophobicity or amphipathicity. Selected peptides were chemically synthesized and characterized, and two distinct types of behavior were observed. Macaque and leaf-eating monkey RL-37 peptides, like other helical antimicrobial peptides found in insect, frog, and mammalian species, were unstructured in bulk solution and had a potent, salt and medium independent antimicrobial activity in vitro, which may be the principal function also in vivo. Human LL-37 and the orangutan, hylobates, and callithrix homologues instead showed a salt-dependent structuring and likely aggregation in bulk solution that affected antimicrobial activity and its medium dependence. The two types of peptides differ also in their interaction with host cells. The evolution of these peptides has thus resulted in distinct mechanisms of action that affect the direct antimicrobial activity and may also modulate accessory antimicrobial functions due to interactions with host cells.

Amino Acid Sequence↗
PubMed1999

Detection of additional structural variation at the FES/FPS system and population data from S. Tomé e Príncipe and North Portugal.

Comparative analysis of heteroduplex patterns on the STR FES/FPS system led to the detection of a new non-consensus allele 10 in the African population of São Tomé e Príncipe. Automated sequencing confirmed a T-->C substitution at position 177 (1stT of the 6th repeat) which was exclusively found in haplotypic combination with base A in the previously described polymorphic position 34. The new substitution was not detected in a sample from North Portugal. Sequence analysis revealed a triplet of inverted bases, from positions 101 to 103, relative to the sequence described in the GeneBank (Accession No. X06292). This work confirms the capacity of heteroduplex analysis in the detection of DNA structural microvariation and emphasises the complementary utility of manual system analysis and semi-automated techniques for a full characterisation of the genetic variability of STRs.

Adult↗
PubMed1996

Structural variation in the alleles of a short tandem repeat system at the human alpha fibrinogen locus.

This paper reports the sequences of 22 alleles identified at the HumFGA (human alpha fibrinogen) short tandem repeat locus in the British Caucasian and Afro-Caribbean populations. Alleles at the lower end of the observed size range were found to increase in size by 4-bp increments with the repeat unit following the pattern TC(TCTT)n. However, 5 alleles were identified that differed in size by 2 bp from the 4 bp increment as a result of the deletion of a TC dinucleotide, or the addition of a TT dinucleotide, immediately prior to the 1st repeat unit. Alleles at the upper end of the observed size range were found to have a more complex repeat unit structure and also exhibited duplication of both 5' and 3' flanking sequences. A nomenclature for the designation of HumFGA alleles is proposed on the basis of this sequence data.

Base Sequence↗
PubMed2006

The enantioseparation of amino acids on a teicoplanin chiral stationary phase using non-aqueous mobile phases after pre-column derivatization with sulfur-containing reagents: the considerations of mobile phase composition and analyte structure variation on resolution enhancement.

Amino acids were derivatized with sulfur-containing reagents in alkaline medium and enantioresolved by HPLC on a teicoplanin chiral stationary phase. Much better resolution was achieved using methanol-based mobile phase compared with elution with acetonitrile-based solvent mixture. The value of selectivity factor for many derivatives examined in the study can be easily several tenths of 100 or even exceed 100 in some cases. This magnitude of resolution is suitable for the preparative-scale application of isolating alpha-amino acid enantiomers in the derivatized form using a short column. The resolution is believed to be a result of the hydrogen bonding and steric hindrance by the nitrogen and sulfur atoms from the isothiocyanatyl fragment of the reagent, respectively, and is enhanced as the fragment is structurally phenylated (e.g. 2,4-difluorophenyl isothiocyanate and others examined in this study). The enhancement is even more significant if the aromatic moiety of the reagent becomes more acidic through halogenation with chlorine or fluorine for the stronger pi-pi interaction. However, this type of enhancement is offset to some extent and sometimes obscured by a chlorinated reagent that is relatively large in size as compared with the fluorinated one. Judging from the chromatographic data and the elution profile, the mechanisms leading to the resolutions are believed to be different under the elution of polar-organic mobile phases (i.e. methanol- and acetonitrile-based mobile phases).

Amino Acids↗
PubMed2005

3D coordination polymers with nitrilotriacetic and 4,4'-bipyridyl mixed ligands: structural variation based on dinuclear or tetranuclear subunits assisted by Na-O and/or O-H...O interactions.

The reactions of Cu(II) with the mixed nitrilotriacetic acid (H3NTA) and 4,4'-bipyridyl (4,4'-bpy) ligands in different metal-to-ligand ratios in the presence of NaOH and NaClO4 afforded two complexes, Na3[Cu2(NTA)2(4,4'-bpy)]ClO4 x 5H2O (1) and [Cu2(NTA) (4,4'-bpy)2]ClO4 x 4H2O (2). The two complexes have been characterized by elemental analysis, IR, XRD, and single-crystal X-ray diffraction. 1 contains a basic doubly negatively charged [Cu2(NTA)2(4,4'-bpy)]2- dinuclear unit which was further assembled via multiple Na-O and O-H...O interactions into a three-dimensional (3D) pillared-layer structure. 2 features a two-dimensional (2D) undulated brick-wall architecture containing a basic doubly positively charged [Cu4(NTA)2(4,4'-bpy)2]2+ tetranuclear unit. The 2D network possesses large cavities hosting guest molecules and was further assembled via O-H...O hydrogen bonds into a 3D structure with several channels running in different directions.

Journal Article↗
PubMed1984

Primary structural variation among serologically indistinguishable DS antigens: the MB3-bearing molecule in DR4 cells differs from the MB3-bearing molecule in DR5 cells.

HLA-DS molecules bearing the MB3 supertypic specificity have been isolated from two DR4 and two DR5 homozygous cell lines by using the monoclonal antibody IVD12 . Limited amino-terminal amino acid sequence analysis of these molecules demonstrates polymorphism of the HLA-DS subregion. Although the distribution of amino-terminal tyrosine residues in the alpha-chains of all IVD12 -reactive molecules was identical, amino-terminal amino acid sequence differences existed between DS beta-chains isolated from these two groups of cell lines bearing different DR specificities. These studies indicate that two DS molecules bearing the same serologic determinant ( MB3 ), although similar to one another, may be structurally distinct.

Amino Acid Sequence↗
PubMed2001

Studies on the structural variations of pentosan polysulfate sodium (NaPPS) from different sources by capillary electrophoresis.

Commercial pentosan polysulfate sodium salts (NaPPS) are highly sulfated polysaccharides derived from beechwood hemicellulose by sulfate esterification with a Mrel range of 1500-6000. The polysaccharide backbone of NaPPS consists of repeating linear units of 1-4 linked beta-D-xylopyranose with laterally substituted 4-methylglucopyranosyluronic acid units glycosidically linked to the 2 position of the main chain at every 10th xylopyranose unit on average. For many years NaPPS has been used for antithrombotic prophylaxis in Europe and interstitial cystitis in the USA and Australia. More recently NaPPS has found veterinary application for the treatment of osteoarthritis and related conditions in domestic animals and is registered for this use in Australia, New Zealand, Canada, UK, Eire, and several Scandanavian countries. At present the use of NaPPS for human disorders is confined to material manufactured by one company. However, for veterinary applications, NaPPS from three manufactures have been described. Since it is well known that the biological activities of sulfated polysaccharides are dependent on their molecular structures we considered it important to characterise these various NaPPS preparations using an established method of analysis. Unfortunately, traditional analytical techniques such as TLC, OR, UV/Vis spectroscopy, and size exclusion chromatography were incapable of providing structural information which would distinguish these NaPPS preparations from each other. In contrast, a capillary zone electrophoresis (CZE) method facilitated characterisation of the different NaPPS by a highly reproducible fingerprint, using a benzene-1,2,4-tricarboxylic acid buffer (8.75 mmol/L, pH = 4.9) with indirect UV detection (lambda = 217 nm) and a special capillary pre-treatment (1 M NaOH for 1 h at 25 degrees C, then running buffer for 120 min at 25 degrees C applying -20 kV). In the present study more than 20 batches of NaPPS from the three manufacturers have been investigated and compared. Minor batch variations were observed to exist for each manufacturer's product however significant differences were detected between NaPPS synthesised by the different manufacturers. Moreover, some preparations showed fingerprint profiles that indicated a more heterogeneous mixture, probably containing other polysaccharides as well.

Buffers↗
PubMed1993

Structural variations in anchoring fibrils in dystrophic epidermolysis bullosa: correlation with type VII collagen expression.

Dystrophic epidermolysis bullosa is characterized by various abnormalities of anchoring fibrils, which are mainly composed of type VII collagen, at the dermal-epidermal junction. To define these changes more clearly, we examined skin samples from 22 patients with different forms of dystrophic epidermolysis bullosa by pre-embedding immunoelectron microscopy using an antibody (LH 7:2) that binds to the NC-1 globular domain of type VII collagen, followed by 1 nm colloidal gold-labeled secondary antibodies and subsequent silver enhancement. In dominant dystrophic epidermolysis bullosa cases, there was only a slight but variable reduction in the immunolabeling density on anchoring fibrils and on the lamina densa, in parts similar to normal human skin. In localized recessive dystrophic epidermolysis bullosa skin, some fibrillar structures just below the lamina densa (and particularly subjacent to hemidesmosomes) had specific antibody labeling despite their lack of resemblance to definitive anchoring fibrils. Immunolabeling with LH 7:2 was also seen within basal keratinocyte endoplasmic reticulum and cytoplasmic vesicles in some dystrophic epidermolysis bullosa patients, usually with milder phenotypic features. Even in the most severe cases of generalized recessive dystrophic epidermolysis bullosa, occasional immunolabeling was found within the lamina densa and on scanty thin filamentous structures at sub-lamina densa sites usually occupied by anchoring fibrils. This study suggests that dystrophic epidermolysis bullosa patients express some type VII collagen NC-1 domain epitopes that may be variably reduced at the dermal-epidermal junction or retained within basal keratinocytes. The clinical heterogeneity in dystrophic epidermolysis bullosa is mirrored by a range of immunoelectron microscopy findings, indicating variability in completeness of anchoring fibril formation and a possible spectrum of underlying type VII collagen structural protein abnormalities.

Adolescent↗
PubMed1976

Correlation between structural variation and activity of murine kidney beta-galactosidase: implications for genetic control.

Two closely linked regulatory genes have been reported to control activity levels of beta-galactosidases in murine tissues. The specific effects of these genes on murine glycolipid metabolism have not been elucidated. A/HeJ kidney 4-methylumbelliferyl-beta-galactosidase exhibited lower thermostability than the corresponding C57BL/6J and SWR/J enzymes. This altered response to heat segregated with the Bgsh allele among progeny derived from backcrosses of F1 (A/HeJ; SWR/J) mice to the respective parental strains. Restriction of the heat-sensitive A/HeJ beta-galactosidase to kidney tissue suggests that it is not determined by the Bgs locus, since the latter appears to be expressed in all tissues. More likely, the Bgs region of chromosome 9 contains a gene cluster consisting of a number of regulatory and structural loci. The proposed structural genes share affinity for the artificial substrates commonly employed for their assay but may differ in their relative affinities for glycosphingolipid substrates. Presence of the Bgsh allele results in an increase of kidney GM1-ganglioside-beta-galactosidase; however, galactosylceramide-beta-galactosidase appears unaffected by this allele.

Animals↗
PubMed1998

Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme.

The hammerhead ribozyme is capable of cleaving RNA substrates at 5' UX 3' sequences (where the cleavage site, X, can be A, C, or U). Hammerhead complexes containing dC, dA, dI, or rG nucleotides at the cleavage site have been studied by NMR. The rG at the cleavage site forms a Watson-Crick base pair with C3 in the conserved core of the hammerhead, indicating that rG substrates inhibit the cleavage reaction by stabilizing an inactive conformation of the molecule. Isotope-edited NMR experiments on the hammerhead complexes show that there are different short proton-proton distances between neighboring residues depending upon whether there is a dC or dA at the cleavage site. These NMR data demonstrate that there are significant differences in the structure and/or dynamics of the active-site residues in these hammerhead complexes. Molecular dynamics calculations were used to model the conformations of the cleavage-site variants consistent with the NMR data. The solution conformations of the hammerhead ribozyme-substrate complexes are compared with the X-ray structure of the hammerhead ribozyme and are used to help understand the thermodynamic and kinetic differences among the cleavage-site variants.

Binding Sites↗
PubMed1988

Structural variations of blood group A antigens in human normal colon and carcinomas.

The blood group A determinant is carried by four basic carrier carbohydrate chains. This paper reports the expression of blood group A variants, as determined by immunohistology with highly specific monoclonal anti-A antibodies, in 18 adenocarcinomas of the distal colon, 4 specimens of normal proximal mucosa from group A persons, and 5 specimens of fetal colonic mucosa. Monoclonal antibodies directed to type 1 chain A, type 1 chain ALeb, type 2 chain A, type 2 chain ALey, and type 3 chain A (repetitive A) were used. In normal mucosa, type 1 chain A and ALeb were expressed in proximal regions. Type 1 chain A was expressed in columnar cells, whereas type 1 chain ALeb was found in goblet cells. Type 2 and type 3 chain A structures were not found in normal adult mucosa. All types of A antigens were detected in adenocarcinomas from the distal colon as well as in normal fetal mucosa. In fetal mucosa, type 1 chain A and ALeb antigens and type 3 chain A antigens were expressed in columnar cells, whereas type 2 chain A and Ley and type 1 chain ALeb antigens were found in goblet cells. The results indicate that blood group A antigens with type 1, 2, and 3 carriers are present in fetal mucosa and adenocarcinomas of distal colon, while epithelial mucosa of normal adult colon is characterized by the exclusive expression of type 1 chain A antigens.

ABO Blood-Group System↗
PubMed1982

Effects of structural variations in synthetic glycolipids upon mitogenicity for spleen lymphocytes, adjuvancy for humoral immune response and on anti-tumour potential.

Synthetic glycolipids prepared by esterification of various sugars and sorbitol, and containing various numbers of saturated or unsaturated fatty acid residues as well as bacterial lipid A and lipopolysaccharide, were tested for mitogenicity of splenic cells of Fischer rats and Swiss mice and for the augmentation of humoral immune response against sheep red blood cells in these species. Subsequently a few of the humoral immune-response-enhancing glycolipids were compared with non-enhancers in their anti-tumour activity against 13762 rat mammary carcinoma in inbred Fischer 344 rats and Ehrlich tumour in Swiss mice. They were given systemically after tumour inoculation and intratumourally in squalene and Tween emulsion after intradermal MAC tumour development. It was observed that certain structural characteristics in glycolipids with respect to the type of sugar, the type and number of fatty-acid residues were needed for their adjuvant action of the humoral arm of the immune response. Although humoral immune-response enhancers were somewhat superior to non-enhancers in their anti-tumour activity, the correlation coefficient demonstrated a lack of significant concordance. It is concluded that glycolipids selected for their ability to augment humoral immune responses against standard antigens need not be suspect as tumour-enhancers on the grounds that they would elicit blocking antibodies in vivo against tumour-associated antigens.

Adenocarcinoma↗
PubMed1984

Sequence-dependent structural variation in single-helical DNA. Proton NMR studies of d(T-A-T-A) and d(A-T-A-T) in aqueous solution.

The two deoxyribotetranucleoside triphosphates d(T-A-T-A) and d(A-T-A-T) were investigated in aqueous solution by one- and two-dimensional proton NMR at 300 and 500 MHz. It is demonstrated that both compounds occur predominantly in the single-helical form. Accurate coupling constants are obtained by computer simulation of several 500-MHz spectra. The data are interpreted in terms of N and S pseudorotational ranges. The geometry of the major S-type conformers displays a clear sequence dependence, as expressed by variation of the endocyclic backbone angle delta (C5'-C4'-C3'-O3'). A simple sum rule is proposed to predict delta variation in single-helical DNA fragments. Comparisons are made with other sequence-dependent geometries as observed in a double-helical B-DNA fragment in the crystalline state. Furthermore, one- and two-dimensional nuclear Overhauser effect (NOE) spectroscopy was carried out on d(T-A-T-A). An inventory is made of the observed intra- and inter-residue NOEs. The NOE data confirm the presence of a highly stacked single-helical conformation of d(T-A-T-A) in solution. No indications are found for the formation of a bulge-out structure as observed for analogous alternating purine-pyrimidine oligoribonucleotides.

Base Sequence↗