PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Structural variation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources
PubMed1991

Structural variations produced in vitro by gonadotrophins and steroid hormones on the cell surfaces of the ovarian epithelium of the chick embryo.

The purpose of the present work was to analyze the structural variations produced "in vitro" by hormones on the cell surfaces of the ovarian epithelium of the chick embryo, in relation to the growth of the left ovary and atrophy of the right one. Explants of both ovaries from embryos at 7 to 19 days of development were separately cultured for 4 days in MEM with 10% of fetal bovine serum (control), and plus 17-beta-estradiol, testosterone propionate, progesterone, FSH, LH or hCG added individually to cultures (experimental). The cultures were processed for their structural, ultrastructural and cytochemical study. In control cultures, membrane differentiations and mucosubstances were similar in both ovaries and at all ages to those in ovo. 17-beta-estradiol produced a greater development of microvilli, junctional complexes and mucin in the epithelial cells and interdigitations in the germ cells of the left ovary, while in the right gonad there was cell regression. Testosterone and progesterone evoked in the left gonad a response similar to that obtained with the estrogen, whereas in the right ovary no changes were observed with respect to controls. FSH led to cellular regression in both ovaries. Finally, with LH or hCG the changes produced in the left ovary were similar to those induced by the estrogen, and in the right one an increase of membrane differentiations and of mucosubstances related to them was found in comparison to controls.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1989

Glucose-6-phosphate dehydrogenase. Characterization of a reactive lysine residue in the Pichia jadinii enzyme reveals a limited structural variation in a functionally significant segment.

Glucose-6-phosphate dehydrogenase from the yeast Pichia jadinii has a reactive lysine residue in a segment of amino acid sequence Ile-Asp-His-Tyr-Leu-Gly-Lys*-Glu-Met-Val-Lys. This structure differs from that of other characterized glucose-6-phosphate dehydrogenases, but outside yeasts the segment is invariant in known mammalian, insect and bacterial forms. Thus, limited structural variation is now defined within yeasts for a part of the protein otherwise strictly conserved, and for which stringent structural requirements probably relate to enzymic mechanisms.

Amino Acid Sequence↗
PubMed1987

Structural variations in the alanine-rich antifreeze proteins of the pleuronectinae.

The sequence and activity of antifreeze proteins from two right eye flounder species were compared to assess the influence of structural variations on antifreeze capacity. The cDNA encoding the major serum antifreeze protein in the yellowtail flounder (Limanda ferruginea) was cloned from liver tissue. Its DNA sequence shows that the precursor to the antifreeze is a 97-residue preproportion. Edman degradation identified the N-terminus of the 48-amino-acid mature serum antifreeze protein and confirmed the sequence of the first 36 residues. A comparison with the previously determined winter flounder antifreeze protein and mRNA sequences shows strong homology through the 5' and 3' untranslated regions and in the peptide region. The mature protein section has the greatest sequence variation. Specifically, the yellowtail antifreeze protein, in contrast to that of the winter flounder, contains a fourth 11-amino-acid repeat and lacks several of the hydrophilic residues that have been postulated to aid in the binding of the protein to ice crystals. Intramolecular salt bridges are present in the antifreeze proteins from both species but in different registries with respect to the 11-amino-acid repeats. On a mass basis the yellowtail flounder antifreeze, though longer than that of the winter flounder, is only 80% as effective at depressing the freezing temperature of aqueous solutions. This lower activity might be due to the reduced number of hydrophilic ice-binding residues per molecule.

Alanine↗
PubMed1986

Demonstration of structural variation in rat incisor dentin as determined by the x-ray Laue method.

Rat incisor dentin was studied by an x-ray micro-Laue method to investigate the relationship between crystal orientation and structural variation in the dentin. The results showed that crystal orientation was very poor in the labial dentin, but that the crystals were well-oriented in the lingual dentin. In the lingual dentin, the axis of crystal orientation was parallel to the tooth axis. It is suggested that the difference in crystal orientation between the lingual and labial dentin is due to the different mode of calcification between the two.

Animals↗
PubMed1991

Swimming navigation and structural variations of the infrapyramidal mossy fibers in the hippocampus of the mouse.

The extent of the infrapyramidal mossy fiber projection in CA3 (IIP-MF) at the midseptotemporal level correlates negatively with two-way avoidance learning and positively with performance in the radial maze, both tasks known to be sensitive to hippocampal lesions. If hippocampal structural variations are causing behavioral variations, one must predict positive correlations between the extent of the IIP-MF and performance in swimming navigation. Thus, the authors studied learning and reversal learning of swimming navigation in mice in which the size of the IIP-MF had been randomized by means of systematic crosses and in 2 mouse strains known for differential infrapyramidal projections (C57BL/6 and DBA/2). In 19 random-bred mice (9 male, 10 female), the extent of the IIP-MF showed negative correlations with swimming time after platform reversal (day 4: r = -0.50, P < .03; day 5 r = -0.73, P < .001), but none during acquisition of the task. In addition, statistical analysis suggested an influence of asymmetrically distributed mossy fiber projections during reversal learning. The strain comparison between 18 DBA/2 and 16 C57BL/6 male mice confirmed these results: no strain difference during days 1-3, and a significantly faster swimming time in the strain C57BL/6 (with large IIP-MF) at day 5 (second day of reversal), associated with significantly more crossings of the former platform location during the early phases of reversal learning. This latter measure was also negatively correlated with asymmetry of the IIP-MF in both strains. Finally, variations of the IIP-MF were correlated partially with adjustment of swimming speed that appeared to depend on size and asymmetry of CA4 as well. Thus, natural variations in the size of the IIP-MF distribution, and, perhaps, of CA4, appear to linearly influence processes directly involved in complex spatial learning.

Animals↗
PubMed2026

Complex structural variation, phylogeny, and disease associations of the mucin pangenome.

Mucins are large glycoproteins that provide hydration and barrier function to epithelial tissues. Although genetically heterogeneous, all mucins harbor a large exon composed of variable number tandem repeats (VNTRs). Short-read sequencing has limited our understanding of mucin VNTR diversity and makes disease association studies challenging. We leverage 296 long-read phased genome assemblies to characterize 14 mucin family members, achieving &#x2265;97% accuracy across 572 haplotypes. Phylogenetic haplogroup analysis reveals extraordinary structural heterozygosity, with MUC4 harboring the greatest allelic diversity (n=240 distinct lengths) and MUC12 the greatest size range (&#x394; = 55,233 bp; 23,080 amino acids). Ten mucins show significant population stratification (pFDR < 0.05). At the MUC4/MUC20 locus, we characterize higher-order structural variation, including a recurrent inversion, copy number variation, and interlocus gene conversion. Optimized genotyping achieves &#x2265;95% haplogroup concordance across 10 loci. We apply this to 4,637 deeply phenotyped cystic fibrosis patients and identify a significant association between short MUC1 VNTRs and severe disease (p=0.0056), demonstrating the pangenome's utility for complex locus genotyping and disease discovery.

Journal Article↗
PubMed2026

Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut.

The cultivated peanut is a crucial global legume crop that is essential for food security and nutrition, particularly in developing regions. However, its limited genetic variation hampers breeding progress and yield improvement. Here we constructed a graph-based pan-genome for peanut, incorporating 14 genomes that represent all 6 peanut varieties. Using this pan-genome, we genotyped 2,320 accessions, covering 88.03% of ICRISAT and 59.21% of USDA core germplasm, enriching valuable resources for genomic studies and breeding. We cataloged genomic structural variations and investigated the role of homoeologous exchanges in population divergence. Through our pan-genome approach, we overcame the challenges of genotyping posed by homoeologous exchanges and identified key genes associated with flowering and dwarfism in peanut. By integrating superior haplotypes and germplasm resources guided by the pan-genome, we further developed high-yield dwarf lines. This work provides essential genomic resources to accelerate functional gene discovery and modern peanut breeding.

Journal Article↗
PubMed2025

Substantial non-homologous recombination and structural variation results from Brassica AABC and CCAB hybrid meiosis.

Meiotic crossovers contribute to genetic diversity and play a crucial role in homologous chromosome segregation. Non-homologous crossovers in Brassica, involving the exchange of genetic material between genomes, can be valuable for transferring novel traits or characteristics between Brassica species. However, there are a limited number of studies that specifically investigate crossover frequencies in populations of interspecific hybrids. We investigated the distribution and frequency of homologous crossover events, as well as non-homologous recombination and structural variation, in hybrids between B. juncea (AABB)&#x2009;&#xd7;&#x2009;B. napus (AACC) (resulting in AABC hybrids; 5 genotypes) and B. napus (AACC)&#x2009;&#xd7;&#x2009;B. carinata (BBCC) (resulting in CCAB hybrids; 4 genotypes). The analysis was performed on individuals derived from microspore culture of both unreduced and reduced gametes produced by the AABC and CCAB hybrids. All AABC and almost all CCAB unreduced gamete-derived individuals and most AABC and CCAB reduced gamete-derived individuals showed copy number variation indicative of non-homologous (A-C) recombination. Additionally, a higher frequency of homologous crossovers, also in centromeric and pericentromic regions, was observed in the diploid genomes of the AABC and CCAB hybrids. Overall, these hybrid types show high frequencies of A-C introgressions, which may be useful in B. juncea or B. carinata introgression breeding, and this increased recombination frequency may help break up existing linkage disequilibrium blocks in the Brassica A and C genomes.

Meiosis↗
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↗
PubMed1987

Evidence for diverse structural variations of the forms of human FSH within and between pituitaries.

The biological activity of FSH in vitro (B-vitro) was compared with its radioimmunological (RIA) activity in 38 pituitary extracts from men and women. The B-vitro method was based upon the estimation of oestradiol produced by cultured Sertoli cells from 10-day-old rats. The mean B-vitro/RIA ratios for FSH of men and young and elderly women were almost identical. The mean values of median charge of the forms of FSH differed significantly between the three groups of human adults. The B-vitro/RIA ratio of different forms of FSH, separated by electrophoresis of 14 individual pituitary extracts, was higher for less negatively charged than for more negatively charged forms. Some forms of FSH with the same charge and separated from different pituitary extracts, e.g. from a young and an elderly woman, had significantly different B-vitro/RIA ratios. This ratio, thus, was not related to the charge per se of the hormone. However, the relation between the B-vitro/RIA ratio and the charge of FSH was similar for individual pituitary extracts when charge was expressed in relation to median charge. The results suggest that different molecular structural variations of FSH are involved in the polymorphisms observed within and between individual pituitaries. In human adults, the variation of FSH between the pituitaries mainly affects the metabolic clearance rate (MCR) of the hormone, whereas the variation within the individual pituitary affects both the MCR of the hormone and its biological effect at the target cell.

Adolescent↗
PubMed1988

Genetic studies of low abundance human plasma proteins. VIII. Inherited structural variation in antithrombin III.

Genetically determined structural polymorphism of antithrombin III has been observed using ultra narrow pH polyacrylamide isoelectric focusing gels, followed by immunoblotting. The products of three alleles at the antithrombin III structural locus have been detected in normal U.S. white and black blood donors. The frequencies of the three alleles, AT III* 1, AT III* 2 and AT III* 3, respectively, are: 0.878, 0.103, 0.019 in whites and 0.916, 0.068, 0.016 in blacks. Family data from a large number of families establish an autosomal codominant pattern of inheritance of the three alleles.

Alleles↗
PubMed1991

Structural variation and (+)-amphetamine-like discriminative stimulus properties.

Rats were trained to discriminate (+)-amphetamine sulfate (5.43 mumol/kg, 1 mg/kg) from saline in a food-reinforced, two-lever drug discrimination paradigm. Side chain variations of the amphetamine molecular structure were analyzed for their effects on the discriminative stimulus properties of this prototype central nervous system stimulant. Partial generalization was observed for the alpha-ethyl homologue of (+)-amphetamine, (+)-AEPEA, and for 2-aminoindan (AI), while 5,6-methylenedioxy-2-aminoindan (MDAI) elicited only saline-appropriate responding. By contrast, 2-amino-1,2-dihydronaphthalene (ADN) and 2-aminotetralin (AT) completely substituted for (+)-amphetamine. Relative to the training drug, ADN was 1/4 as potent and AT was 1/8 as potent. The S-(-)-isomer of ADN was found to be responsible for the (+)-amphetamine-like discriminative properties of the racemate. The results suggest that constraining or extending the alpha-alkyl substituent of (+)-amphetamine has a deleterious effect on the ability of the resulting analogue to adopt the active conformation of (+)-amphetamine, thereby diminishing its characteristic discriminative stimulus properties.

Animals↗
PubMed1992

Three-dimensional structure of Gln25-ribonuclease T1 at 1.84-A resolution: structural variations at the base recognition and catalytic sites.

The structure of the Gln25 variant of ribonuclease T1 (RNase T1) crystallized at pH 7 and at high ionic strength has been solved by molecular replacement using the coordinates of the Lys25-RNase T1/2'-guanylic acid (2'GMP) complex at pH 5 [Arni et al. (1988) J. Biol. Chem. 263, 15358-15368] and refined by energy minimization and stereochemically restrained least-squares minimization to a crystallographic R-factor of 14.4% at 1.84-A resolution. The asymmetric unit contains three molecules, and the final model consists of 2302 protein atoms, 3 sulfates (at the catalytic sites), and 179 solvent water molecules. The estimated root mean square (rms) error in the coordinates is 0.15 A, and the rms deviation from ideality is 0.018 A for bond lengths and 1.8 degrees for bond angles. Significant differences are observed between the three molecules in the asymmetric unit at the base recognition and catalytic sites.

Amino Acid Sequence↗
PubMed2026

European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.

European Ash (Fraxinus excelsior) is a keystone tree species, whose populations are being decimated by ash dieback disease (ADB) - better characterisation of genetic variants associated with low susceptibility to the disease is needed. Here, we develop a F. excelsior pangenome to more fully capture sequence variability within this species compared with a linear reference genome, using a geographically diverse set of fifty F. excelsior samples. We identify 362,965 structural variants (SVs), including 174&#x2009;Mb of sequence absent from the linear reference genome (22% of the linear reference size), and identify 3,412 high-confidence dispensable genes (those present only in some individuals). We use the pangenome to analyse existing genomic data from over 1,200 individuals, revealing 220 single nucleotide polymorphisms (SNPs) showing consistent allele frequency shifts between healthy individuals and those highly damaged by ADB, across UK seed sources, explicitly demonstrating the existence of a shared genetic component to low ADB susceptibility.

Polymorphism, Single Nucleotide↗
PubMed1990

Structural variation in the nasal bone region of European moose (Alces alces L.).

The ontogeny of typical (normal) nasal bone region of the European moose (Alces alces L.) and the 3 variants of the pattern, was studied. The variants, named as "extra bone type", "punctured type" and "open type" referring the morphology of the internasal suture, were originally observed in Finnish male and female moose skulls in 1971. All of the variants were later found in hunting trophy exhibitions presenting male moose trophies from Sweden, Norway, Baltic Republics of USSR and Poland. The frequencies of the variants showed regional differences. By using histological, radiological and OTC bone labelling methods, all of the nasal bone types were observed in this study in embryonal (N = 36), newborn (N = 21), juvenile (N = 38) and adult (N = 12) moose. Two twin embryos showed different nasal bone structure. The variation is considered to be of congenital origin.

Animals↗
PubMed1989

The influence of structural variations in the F- and FG-helix of the beta-subunit modified oxyHb-NES on the heme structure detected by resonance Raman spectroscopy.

The dispersion of the depolarization ratio of two prominent Raman lines (1,375 cm-1 and 1,638 cm-1) of oxyhemoglobin-N-ethyl succinimide have been examined for pH values between pH = 6.0 and 8.5. Both exhibit a significant pH dependence. Calculation of the Raman tensor in terms of a fifth-order time dependent theory provides information about the pH-dependence of parameters reflecting symmetry classified distortions of the prosthetic heme group. To correlate these distortions with the functional properties of the molecule the following protocol was used: 1) An allosteric model suggested by Herzfeld and Stanley (1974) has been applied to O2-binding curves measured at different pH values between 6.5 and 9.0. From this calculation one obtains both, the energy differences between different molecular conformations and the equilibrium constants of oxygen and proton binding. 2) A titration model was formulated relating each conformation of a molecule to a distinct set of distortion parameters of the heme group. 3) The distortion parameters resulting from the analysis of our Raman data were assigned as an effective value due to incoherent superposition of the distortion parameters related to the different titration states. The application of this procedure yields an excellent reproduction of the pH-dependent effective distortion parameters of both Raman lines investigated. It is shown that the protonation of two tertiary effector groups located in the beta-subunits affect the symmetry of the heme in a contrary manner: the protonation of a His-residue (pK = 8.2, probably His(FG4) beta) causes a symmetric position of the proximal imidazole thus lowering the perturbations of the heme core. Further it influences the interaction between amino acid residues of the heme cavity and pyrrole side chains (probably Val(FG5) beta-vinyl (pyrrole 3) thus causing a decrease of the distortions related to the peripheral part of the heme. In contrast, the protonation of Lys (EF6) beta causes a tilt position of the proximal imidazole and an increase of asymmetric perturbations of the heme core, whereas the interaction between the pyrrole side chains and the heme cavity is weakened. Our results are consistent with stereochemical predictions of Moffat (1971) concerning the existence of a H-bond between His(FG4) beta and Cys(F9) beta.

Adult↗
PubMed1988

Ribosomal gene structure, variation and inheritance in maize and its ancestors.

We have examined the structure of nuclear genes coding for ribosomal RNAs in maize and its wild relatives, the teosintes and Tripsacum. Digestion of the rDNA (genes coding for 18S, 5.8S and 26S RNAs) with 15 restriction endonucleases (with six base pair recognition sites) yields essentially a single map for the approximately 10,000 repeat units within an individual plant or species. Both length and site variation were detected among species and were concentrated in the intergenic spacer region of the rDNA repeat unit. This result is in agreement with patterns of rDNA change observed among wheat and its relatives (Triticeae), and among vertebrate species. Digestion of these nuclear DNAs with BamHI and subsequent hybridization with a 5S RNA gene-specific probe allowed determination of the size of the 5S gene repeat unit in maize, teosintes, and Tripsacum. Groupings in the genus Zea were characterized by distinct repeat unit types five Tripsacum species examined shared a 260 base pair major repeat unit type. Additionally, several other restriction endonuclease cleavage patterns differentiated among the 5S DNAs within the genus Zea. The rDNA and 5S DNA restriction site variation among the species can be interpreted phylogenetically and agrees with biochemical, karyotypic, and morphological evidence that places maize closest to the Mexican teosintes. For both gene arrays, contributions from each parental genome can be detected by restriction enzyme analysis of progeny from crosses between maize and two distantly related teosintes, Zea luxurians or Zea diploperennis, but certain teosinte arrays were underrepresented in some of the hybrids.

Blotting, Southern↗