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PubMed1992

Growth cones and structural variation of synaptic end-bulbs in the cochlear nucleus of the adult cat brain.

To explore the potential for structural variation and new growth at the synapse, we studied the morphological patterns of the end-bulbs of cochlear nerve axons in adult cats by using rapid Golgi, reduced silver, and electron microscopic methods. Horseradish peroxidase labeling of these endings in the anterior division of the antroventral cochlear nucleus was produced by anterograde transport following injection into the cochlea. Three types of end-bulbs were distinguished, regardless of method: reticular, coalescent, and ringed forms, all synapsing on spherical bushy cells. The reticular variety corresponds to the classically described end-bulb and constitutes the majority in all regions of the tonotopic map. The ringed end-bulb, described here for the first time, forms an excitatory synaptic cuff around the base of a bushy cell's main dendrite; these endings were localized to the region receiving cochlear input in the 1-6 kHz range, which is used in vocalization. The coalescent ending forms a small fraction of the end-bulb population throughout the region studied. The findings raise the possibility of functional differences between these synaptic types. Growth cones and retraction clubs were present on most, if not all, of the end-bulbs in every adult cat studied. A systematic survey of the end-bulb patterns revealed a continuous gradient of variation, in which each synaptic type forms a distinct mode. These findings lead us to hypothesize that the end-bulbs are in a continual state of structural and functional flux. These endings should prove useful for studies on the modifiable properties of central synapses.

Animals↗
PubMed1986

Prosomes. Ubiquity and inter-species structural variation.

The "prosomes", a novel type of ubiquitous ribonucleoprotein particle of extraordinary stability and of defined electron microscopical structure, have been characterized in several cell types and species. Identified as a 19 S sub-component of free mRNA-protein complexes, including globin and other repressed mRNA, in the cytoplasm of duck, mouse and HeLa cells, they were previously found to inhibit protein synthesis in vitro. In all cells studied, electron microscopy shows an identical, seemingly ring-like but rather raspberry-shaped particle of 12 nm diameter, resistant to EDTA and 1% (w/v) Sarkosyl. Two-dimensional electrophoretic analysis of prosomal proteins shows a characteristic pattern in the 19,000 to 35,000 Mr range of pI 4 to 7, with an additional 56,000 Mr component specific to avian species. The prosomes found in globin mRNA-protein complexes contain about 25 protein components, 16 of which have identical molecular weight and pI values in duck and mouse, and which are also found in the prosomes of the heterogeneous free mRNPs of HeLa cells. Seral and monoclonal antibodies raised in mice against the prosomes of duck erythroblasts cross-react with some of the proteins of the mouse and HeLa cell particles. Prosomes isolated from duck and mouse globin mRNP, both contain small cytoplasmic RNAs of 70 to 90 nucleotides, which represent about 15% of the particle mass. The molecular weight and the 3'-terminal oligonucleotide of each one of these small cytoplasmic RNAs are identical in the two animal species; fingerprints of their oligonucleotides generated by RNase T1 show that more than 80% of spots are identical. In contrast, the prosomes of HeLa cells, associated with a large population of repressed mRNA, contain at least 12 small cytoplasmic RNA species. All prosomal RNAs tested so far hybridize to mRNA. The data available indicate that prosomes constitute a novel class of ubiquitous cellular ribonucleoprotein complexes, present in the nucleus and cytoplasm that, in its structural variations shown here, reflects function and species.

Animals↗
PubMed1989

Phenotypic effects of apolipoprotein structural variation on lipid profiles. IV. Apolipoprotein polymorphisms in a small group of black women from the healthy women study.

Structural variation in apolipoprotein E has been shown to influence lipid and lipoprotein concentrations. The purpose of the present study was to investigate several apolipoproteins in a group of Black women from the Healthy Women Study (HWS). HWS is a community-based prospective study of 541 premenopausal women who are being followed through the menopause to determine the influence of biological, genetic, and psychosocial phenomenon on cardiovascular risk factors. Of the 541 subjects, 48 are Black. Serum from most of these 48 Black women was used to type seven apolipoproteins (APO A-I, APO A-II, APO A-IV, APO C-II, APO D, APO E, and APO H). Five of these apolipoproteins are polymorphic in Blacks (APO A-IV, APO C-II, APO D, APO E and APO H). Only two and three individuals, respectively, were heterozygous at the APO D and APO C-II loci. APO A-IV, E, and H exhibited more variation, however, only APO E phenotypes could be used for statistical analyses. Three common phenotypes, APO E 3-2, APO E 3-3, and APO E 4-3, were used in analysis of variance on four quantitative lipid variables. Despite small numbers, the effect of APO E phenotype was apparent. The APO E 3-2 phenotype showed reduced average levels of total cholesterol, apolipoprotein B (APO B) and low-density lipoprotein cholesterol (LDLc), and the APO E 4-3 phenotype showed increased levels (P less than or equal to .0497). The APO E3-3 homozygote was intermediate on all three. Because of small numbers in the cells of APO A-IV and APO H phenotypes, these were not analyzed with respect to quantitative lipids.

Adult↗
PubMed2026

Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.

Genomic structural variants (SVs) are major sources of genetic variation and have profound impacts on phenotypic traits. However, their functional effects remain largely unexplored in soybean. Here, we resequence 940 soybean accessions. Together with 44 publicly available datasets, we identify 602,281 SVs. Using a graph-based genome, we detect an additional 58,760 presence/absence variations (PAVs) that broadly affect gene expression. Population genomic analyses reveal that SVs serve as a core driving force for soybean domestication and improvement. Integrating SVs with QTLs for oil and protein content, and performing GWAS on 27 traits, we identify key functional SVs. These include transposable element insertions altering seed coat color, multiple insertions within a cytochrome P450 gene modifying flower and hypocotyl color, and a GmMATE1 deletion enhancing seed size. Together, our study establishes a comprehensive SV map of soybean, offering a valuable resource for dissecting the genetic basis of complex traits to accelerate molecular breeding.

Glycine max↗
PubMed1983

Structural variations and optional introns in the mitochondrial DNAs of Neurospora strains isolated from nature.

Mitochondrial DNAs from ten wild-type Neurospora crassa, Neurospora intermedia, and Neurospora sitophila strains collected from different geographical areas were screened for structural variations by restriction enzyme analysis. The different mtDNAs show much greater structural diversity, both within and among species, than had been apparent from previous studies of mtDNA from laboratory N. crassa strains. The mtDNAs range in size from 60 to 73 kb, and both the smallest and largest mtDNAs are found in N. crassa strains. In addition, four strains contain intramitochondrial plasmid DNAs that do not hybridize with the standard mtDNA. All of the mtDNA species have a basically similar organization. A 25-kb region that includes the rRNA genes and most tRNA genes shows very strong conservation of restriction sites in all strains. The 2.3-kb intron found in the large rRNA gene in standard N. crassa mtDNAs is present in all strains examined, including N. intermedia and N. sitophila strains. The size differences between the different mtDNAs are due to insertions or deletions that occur outside of the rRNA-tRNA region. Restriction enzyme and heteroduplex mapping suggest that four of these insertions are optional introns in the gene encoding cytochrome oxidase subunit I. Mitochondrial DNAs from different wild-type strains contain zero, one, three, or four of these introns.

Chromosome Mapping↗
PubMed1988

The characterization of structural variations within a crystal field.

The technique of correlation averaging is refined by the use of multivariate statistical analysis and classification. The refined method can deal with the presence of structural variations within a crystal field. A low-dose image of a crotoxin crystal embedded in ice is used to demonstrate that crystallographic structural parameters characterizing the different areas of such a crystal with varying structure can be extracted rigorously and reproducibly.

Analysis of Variance↗
PubMed1982

Trabecular bone structural variation in biopsy sites of the beagle ilium.

Iliac trabecular bone sites were studied in 2 male and 2 female adult beagles to determine normal structural variability among different sites, and to identify transilial biopsy sites with minimum structural variation. Only sites that provided adequate amounts of trabecular bone were studied. Trabecular bone area and perimeter were measured on microradiographs of ground sagittal sections using a Quantimet 720 image analyzer, and percent bone, perimeter to area ratio, and mean trabecular width were calculated. Over 100% variation was found in the parameters studies among sections from different sites within the same animal. However, variability was minimal among sections obtained more than 2 mm from the lateral or medial cortex within the most caudal sites evaluated. Two sites appropriate for sampling with an 8 mm trephine were identified as being centered over the following points: (a) a point 7 mm caudal to the cranial dorsal spine and 7 mm ventral to the tuber sacrale, and (b) a point 7 mm caudal to the cranial ventral spine and 7 mm dorsal to the tuber coxae. Comparison of data obtained from males and females indicated that sampling variation may also be reduced by using dogs of one sex and by preferential use of males.

Animals↗
PubMed2025

SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies.

MOTIVATION: We are now in the era of being able to routinely generate highly contiguous (near telomere-to-telomere) genome assemblies of human and nonhuman species. Complex structural variation and regions of rapid evolutionary turnover are being discovered for the first time. Thus, efficient and informative visualization tools are needed to evaluate and directly observe structural differences between two or more genomes. RESULTS: We developed SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process these alignments. The tool facilitates the characterization of complex structural variants in the context of sequence homology helping resolve the mechanisms underlying their formation. AVAILABILITY AND IMPLEMENTATION: SVbyEye is available on GitHub (https://github.com/daewoooo/SVbyEye) and via Zenodo (https://doi.org/10.5281/zenodo.15303553).

Software↗
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↗
PubMed1983

Evidence for minor structural variations of class II genes in wild and inbred mice.

We organized 29 B10.W lines into eight antigenic groups on the basis of similarities in the antigenic phenotypes of their class II antigens. Tryptic peptide fingerprint comparisons of class II antigens in different antigenic groups detected structural variations in 30 to 60% of the tryptic peptides. In contrast, less than 10% of the tryptic peptides were distinguishable in comparisons of class II antigens within the same antigenic group. These results suggest structurally discrete allelic families of class II genes exist in wild mouse populations.

Animals↗
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↗
PubMed1983

Sequence-dependent structural variations in two right-handed alternating pyrimidine-purine DNA oligomers in solution determined by nuclear Overhauser enhancement measurements.

A 500 MHz 1H-n.m.r. study on two right-handed self-complementary double-stranded alternating pyrimidine-purine oligodeoxyribonucleotides, 5'dCGTACG and 5'dACGCGCGT, is presented. Using the proton-proton nuclear Overhauser effect, proton resonances are assigned by a sequential method and a large number of interproton distances, both intra- and internucleotide, are determined (113 for 5'dCGTACG and 79 for 5'dACGCGCGT). The general procedure required to solve the three-dimensional solution structures of oligonucleotides from such distance data is outlined and applied to these two oligonucleotides. In the case of both oligonucleotides the overall solution structure is that of B DNA, namely a right-handed helix with a helical rise of approximately 3.3 A, 10 bp per turn and the base pairs approximately perpendicular to the helix axis. In the case of 5'dCGTACG, subtle local structural variations associated with the pyrimidine and purine nucleotides are superimposed on the overall structure but the mononucleotide repeating unit is preserved. In contrast, 5'dACGCGCGT has a clear alternating structure with a dinucleotide repeat, alternation occurring in the local helical twist and the glycosidic bond, sugar pucker and phosphodiester backbone conformations.

DNA↗
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↗
PubMed1966

Immunoglobulin structure: variation in the sequence of Bence Jones proteins.

Analysis of the amino acid sequence of one Bence Jones protein is almost comtplete. Many points of interchange occur in the amino terminal. portion of the molecule relative to partial-sequence data for other proteins. Most, but not all, are, compartible with one-step mutations. Such structural variation in immunoglobulin light chains may result from many related genes.

Amino Acid Sequence↗
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↗