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At least 199 records · Page 11Linked to original sources
PubMed1989

Multinuclear NMR studies of DNA hairpins. 2. Sequence-dependent structural variations.

The solution conformation of three related DNA hairpins, each with five bases in the loop, is investigated by proton and phosphorus 2D NMR methods. The sequences of the three oligomers are d(CGCGTTGTTCGCG), d(CGCGTTTGTCGCG), and d(CTGCTCTTGTTGAGCAG). One pair of hairpins shares the same stem sequence but differs in the loop, and the appearance of an unusual phosphate torsion in the stem is found to depend on the sequence in the loop of the hairpin. The second pair of hairpins shares the same loop region but differs in the stem sequence in that the base pair which closes the loop is a C-G or G-C pair. The pattern of NOEs reveals that the stacking arrangement in the loop region depends on the base pair that closes the stem. These results suggest that hairpin loop conformation and dynamics are sensitive to small changes in the loop and adjacent stem sequences. These findings are discussed in relation to sequence-dependent thermodynamic changes that have been observed in RNA hairpins.

Base Sequence↗
PubMed1999

Distribution and structural variation of arabinoxylans in common wheat mill streams.

In 19 wheat-milling fractions total pentosan content, calculated as 0.88 x (% L-arabinose + % D-xylose), varied between 1.44 and 30.66% on dry matter (dm). It increased with ash content once the latter exceeded 0.6% (dm basis). Water-extractable arabinoxylans were recovered by saturating water extracts to 65% ethanol. Their contents in the milling fractions varied between 0.35 and 1.38%, and above 0.6% ash content also increased with this parameter. Their L-arabinose-to-D-xylose ratios ranged between 0.65 and 0.39, with the lowest values found for the fractions with highest ash content, indicating that the ash-rich tissues contain more arabinoxylans that are less branched. (1)H NMR spectroscopy revealed that the decrease in L-arabinose-to-D-xylose ratio was accompanied by an increase in unsubstituted xylose residues and a decrease in disubstituted xylose residues, while the contents of monosubstituted xyloses were virtually constant.

Industry↗
PubMed2000

Extended structural variation of a pentanucleotide repeat in the GSTP1 gene: characterisation in a normal population and in thyroid and gastric tumours.

The promoter region of the human GSTP1 gene contains a polymorphic short tandem repeat (STR) locus consisting of pentanucleotide repeat units (ATAAA). In this work we report the existence of a total of 26 alleles in a Caucasian population. While differences in size (ranging from one to five base pairs) were responsible for the major variation, in five size-defined classes, two alternative sequences were found. Automatic fragment sizing and sequencing analysis revealed that this polymorphism is of a highly complex nature in contrast with previous reports. A genetic population study was carried out on a random sample from Portugal showing no deviation from Hardy-Weinberg equilibrium. Somatic instability studies were also performed on gastric and thyroid tumours using this STR: no instability was detected in thyroid tumour tissues when compared with their normal counterpart but in gastric tumour tissues microsatellite instability (MSI) was detected in 9.6% of the cases and loss of heterozygosity (LOH) also in 9.6% of the cases studied. The results obtained with GSTP1 in gastric cancer were compared with previously reported data on MSI using BAT-26 and several dinucleotide repeat markers.

Alleles↗
PubMed1986

Structural variations in actins. A study of the immunological reactivity of the N-terminal region.

The antigenicity of the N-terminal region of skeletal-muscle actin was analysed. Two epitopes, corresponding to the 1-7 and 18-28 sequences, were determined. The antibodies specific for the first epitope discriminate skeletal-muscle actin from cardiac-muscle and smooth-muscle actins. The antibodies specific for the second epitope interact with all the actins tested, ranging from invertebrate to higher-vertebrate actins.

Actins↗
PubMed1980

Evidence for structured variation in self-renewal capacity within long-term bone marrow cultures.

Bone marrow pluripotent stem cells (CFUs) demonstrate capacity for both proliferation and differentiation. The proliferative capacity of CFUs has been measured by serial transplantability and by the Rs, a measurement of CFU production in a single 14-day transfer. In the present study, the self-renewal capacity fo both adherent and nonadherent CFUs from long-term bone marrow cultures was measured. Culture conditions were established such that nonadherent cells were derived from the adherent cell layer. Both adherent and non-adherent cells produced spleen colonies, demonstrating that significant proliferative potential was present in both locations; however, at all times in culture, the CFUs within the adherent stromal cell layer had a significantly greater self-renewal capacity than did the nonadherent CFUs. During the initial establishment of the cultures, the self-renewal capacity of the adherent CFUs decreased as the total number of CFUs per flask increased. After 3 weeks in culture, the self-renewal potential of the adherent CFUs stabilized and was maintained. These results suggest two different mechanisms of stem cell proliferation. In order to increase the most primitive stem cell pool size, there was initial proliferation of early stem cells with a concomitant decrease in self renewal capacity. Once this pool was established, the self-renewal capacity of the adherent CFUs maintained for 13 weeks in culture suggests that CFU production and cell maintenance were achieved by clonal succession.

Animals↗
PubMed1967

Structural variations during mitosis in the chick embryo.

Selected tissues from chick embryos were fixed in 2% glutaraldehyde and 1% OsO(4), both buffered at pH 7.6 with Veronal-acetate, and were embedded in Maraglas or Araldite. Two types of cell division have been noted. Generally, epithelial cells divide predominantly by a shortening of the chromosome-to-pole distance rather than by spindle elongation; mesenchymal cells undergo extensive spindle elongation. The presence of numerous continuous microtubules in cells that undergo extensive spindle elongation functionally implicates these tubules in the elongation process. In most embryonic epithelia, the cleavage furrow converges to a fixed site forming a mid-body near the anchoring desmosomes at the free surface; symmetrical furrow formation is typical of mesenchymal cells which lack desmosomes. The hypothesis of cleavage furrow formation and the fate of the mid-body that is formed during cytokinesis are discussed.

Animals↗
PubMed1990

Sequence-dependent structural variations of DNA revealed by DNase I.

Two global helix parameters important for DNA-DNase I interaction are the geometry of the minor groove and the DNA stiffness that resists bending toward major groove. Thus, local averaging of P-O3' bonds cutting frequencies (InP) reflects global helix parameters revealed by DNase I. Using the approximation that locally averaged InP values depend only on the type of the dinucleotide steps involved in the region of interaction, we calculated the collective contribution (sigma Dd) for ten different dinucleotide steps. Our results suggest that, at the first approximation, global varying helix parameters revealed by DNase I, might be predicted from sequence. Obtained sigma Dd function can be used as a sequence-dependent measure of protein-induced DNA flexure in the direction towards the major groove, which is usually connected to widening of the minor groove. In the course of analysis of Mg2+ and Mn2+ dependent DNase I digestions, no significant difference was found, in spite of the supposed differences in enzyme activity. These results suggest that if the second Mn2(+)-dependent active site exists, its activity is lower than that of the first one.

Base Sequence↗
PubMed1987

Antigenic and structural variation of the p28 core polypeptide of goat and sheep retroviruses.

The p28 core polypeptides of four isolates of caprine arthritis-encephalitis virus (CAEV) from goats was compared with those of visna virus (VV) and progressive pneumonia virus (PPV) from sheep. Monoclonal antibodies recognized p28 epitopes common to all six retrovirus isolates, a p28 epitope on four CAEV isolates, but not VV and PPV isolates, a p28 epitope on four CAEV isolates and VV, but not PPV and a p28 epitope unique to the CAEV isolate used for immunizing the mouse spleen donor. Comparison of two-dimensional maps of tyrosine containing tryptic peptides of p28 demonstrated that three CAEV isolates had similar maps while a fourth CAEV isolate, VV and PPV had several different from the three closely related CAEV p28s and from each other.

Animals↗
PubMed1983

Structural variations in pili expressed during gonococcal infection.

Gonococci were cultured from the urethra of male patients and from the cervix and urethra of their female partners. SDS-PAGE of cell lysates from within each group of consorts showed that outer membrane protein I remained constant but considerable variations were seen in the apparent molecular weight of protein II. Pili were purified from the isolates of some groups of consorts. In each case the pili expressed by the isolates from the female cervix and urethra differed in subunit molecular weight and were usually also distinct from the pili expressed by the isolate from the male partner.

Bacterial Outer Membrane Proteins↗
PubMedDate not supplied

Structural variations in the H-2 genes of AKR lymphomas.

K36.16 is an AKR H-2k thymoma which expresses an aberrant H-2Dd-like allospecificity, does not have a detectable amount of the H-2Kk syngeneic antigen and grows very easily in syngeneic mice. By DNA-mediated gene transfer experiments, we were able to obtain transformed clones which do express the H-2Kk molecules and are rejected by AKR mice. Southern hybridization was performed to assess whether any gross changes had occurred in the K36.16 H-2K locus or elsewhere in the MHC, which might explain the lack of H-2K expression and/or the presence of the aberrant H-2Dd-like allospecificity. Specific H-2 class I DNA probes were used to compare the K36.16 genomic DNA with normal AKR thymus DNA after digestion with a variety of restriction enzymes. After hybridization with the pH-2IIa probe a 2.8 kb 'Hind III' fragment was identified in the K36.16 genomic DNA which is absent from AKR DNA. The pH-2IIa probe detects the third, transmembrane and cytoplasmic domains of class I genes. Although these changes are indicative of MHC genome modifications it is not yet possible to link these specific Southern blot pattern variations with the phenotypic changes mentioned above.

Animals↗
PubMed1999

Structural variation of the distal condyles of the third metacarpal and third metatarsal bones in the horse.

This study examined 3-dimensional (3D) distribution of sectors with contrasting density in the equine third metacarpal (McIII) and third metatarsal (MtIII) bones with a view to explaining the aetiology of distal condylar fractures. Macroradiography and computed tomographic (CT) imaging were used in the nondestructive study of bones obtained from horses, most of which were Thoroughbreds in race training. Distal condylar regions of McIII and MtIII were also studied in microradiographs of 100 microm thick mediolateral sections cut perpendicular to the dorsal and palmar/plantar articular surfaces. Qualitative and quantitative results from all methods used (radiography, CT and microradiographic stereology) demonstrated a densification (sclerosis) of subchondral bone located in the palmar/plantar regions of the medial and lateral condyles of both McIII and MtIII. Substantial density gradients between the denser condyles and the subchondral bone of the sagittal groove were shown to equate with anatomical differences in loading intensity during locomotion. It is hypothesised that such differences in bone density results in stress concentration at the palmar/plantar aspect of the condylar grooves, which may predispose to fracture.

Animals↗