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PubMed1982

Genetic heterogeneity of prothrombin (FII).

A new procedure for the electrophoresis and localization of prothrombin is described. This technique has revealed three allelic variants at the prothrombin structural locus (FII). One of these alleles (FII4) reaches polymorphic frequencies in some Pacific Island populations. Investigation of the activated products of the three variant prothrombins has demonstrated that, in each case, the structural variation is located on a profragment and not on the enzymically active thrombin molecule.

Alleles↗
PubMed1985

Reversible dihydropyridine isothiocyanate binding to brain calcium channels.

Voltage-dependent calcium channels from ileal smooth muscle can be affinity-labeled with a [3H]dihydropyridine isothiocyanate radioligand. We examined the binding of this agent to brain membranes, to compare the properties of calcium channel drug binding sites in brain with those previously described in ileum. In brain, the [3H]dihydropyridine isothiocyanate labels sites that correspond in number and pharmacologic characteristics to binding sites for the classic calcium entry blocker, [3H]nitrendipine. However, in contrast to the covalent nature of dihydropyridine isothiocyanate binding in ileum, brain calcium channels are labeled reversibly. This difference in binding properties may reflect structural variations in voltage-dependent calcium channels in different tissues.

Animals↗
PubMed1985

Purification of somatostatin from frog brain: coisolation with retinal somatostatin-like immunoreactivity.

Somatostatin-like immunoreactivity (SLI) was purified from frog brain and retina, and the structure of the brain peptide was determined. Frog brain (101 g) and retinal (45 g) tissues were extracted with 3% acetic acid, yielding 9.6 and 0.44 nmol of SLI, respectively. SLI was further purified by chromatography on a somatostatin immunoaffinity column followed by sequential application to reverse-phase C-18 HPLC columns. The brain and retinal peptides, purified roughly 100,000-fold with net yields of 7.5 and 2.3%, respectively, appeared identical in the final steps of purification. The amino acid sequence of brain SLI, as determined by a gas-phase automated Edman degradation technique, was as follows: Ala-Gly-(Cys)-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-(Cys). Our data indicate that despite structural variations in somatostatins of other lower vertebrates, the amino acid sequence of frog brain and, by deduction, retinal SLI is identical to that of somatostatin tetradecapeptide. These findings support the physiological relevance of studies directed at elucidating the neurotransmitter function of somatostatin using the well-established models of frog brain and retina.

Amino Acid Sequence↗
PubMed1993

Thermodynamics of antagonist binding to rat muscarinic M2 receptors: antimuscarinics of the pridinol, sila-pridinol, diphenidol and sila-diphenidol type.

1. We studied the effect of temperature on the binding to rat heart M2 muscarinic receptors of antagonists related to the carbon/silicon pairs pridinol/sila-pridinol and diphenidol/sila-diphenidol (including three germanium compounds) and six structurally related pairs of enantiomers [(R)- and (S)-procyclidine, (R)- and (S)-trihexyphenidyl, (R)- and (S)-tricyclamol, (R)- and (S)-trihexyphenidyl methiodide, (R)- and (S)-hexahydro-diphenidol and (R)- and (S)-hexbutinol]. Binding affinities were determined in competition experiments using [3H]-N-methyl-scopolamine chloride as radioligand. The reference drugs were scopolamine and N-methyl-scopolamine bromide. 2. The affinity of the antagonists either increased or decreased with temperature. van't Hoff plots were linear in the 278-310 degrees K temperature range. Binding of all antagonists was entropy driven. Enthalpy changes varied from large negative values (down to -29 kJ mol-1) to large positive values (up to +30 kJ mol-1). 3. (R)-configurated drugs had a 10 to 100 fold greater affinity for M2 receptors than the corresponding (S)-enantiomers. Enthalpy and entropy changes of the respective enantiomers were different but no consistent pattern was observed. 4. When silanols (R3SiOH) were compared to carbinols (R3COH), the affinity increase caused by C/Si exchange varied between 3 and 10 fold for achiral drugs but was negligible in the case of chiral drugs. Silanols induced more favourable enthalpy and less favourable entropy changes than the corresponding carbinols when binding. Organogermanium compounds (R4Ge) when compared to their silicon counterparts (R4Si) showed no significant difference in affinity as well as in enthalpy and entropy changes. 5. Exchange of a cyclohexyl by a phenyl moiety was associated with an increase or a decrease in drug affinity (depending on the absolute configuration in the case of chiral drugs) and generally also with a more favourable enthalpy change and a less favourable entropy change of drug binding. 6. Replacement of a pyrrolidino by a piperidino group and increasing the length of the alkylene chain bridging the amino group and the central carbon or silicon atom were associated with either an increase or a decrease of entropy and enthalpy changes of drug binding. However, there was no clear correlation between these structural variations and the thermodynamic effects. 7. Taken together, these results suggest that hydrogen bond-forming OH groups and, to a lesser extent, polarizable phenyl groups contribute significantly to the thermodynamics of interactions between these classes of muscarinic antagonists and M2 muscarinic receptors.

Animals↗
PubMed2006

Diversity of temperate bacteriophages induced in bovine and ovine Mannheimia haemolytica isolates and identification of a new P2-like phage.

The diversity of temperate bacteriophages was examined in 32 Mannheimia haemolytica, six Mannheimia glucosida and four Pasteurella trehalosi isolates. Phage particles were induced and identified by electron microscopy in 24 (75%) M. haemolytica isolates, but in only one (17%) M. glucosida and one (25%) P. trehalosi isolate. The M. haemolytica phages were relatively diverse as seven Siphoviridae, 15 Myoviridae and two Podoviridae-like phages were identified; the Myoviridae-type phages also exhibited structural variation of their tails. The bacteriophages induced in M. glucosida and P. trehalosi were of the Myoviridae type. Restriction endonuclease (RE) analysis identified nine distinct RE types among the M. haemolytica bacteriophages, providing further evidence of their relative diversity. A limited number of phages caused plaques on indicator strains and the phages exhibited a narrow host range. A subgroup of 11 bovine serotype A1 and A6 isolates contained Myoviridae-type phages of the same RE type (type A), but these differed in their abilities to infect and form plaques on the same panel of indicator strains. A P2-like phage (phiPHL213.1), representative of the RE type A phages, was identified from the incomplete M. haemolytica genome sequence. The phiPHL213.1 genome contains previously unidentified genes and represents a new member of the P2 phage family.

Animals↗
PubMed1993

Multinucleated fibroblastic cells in the periodontal ligaments of aged rats.

Using 12- to 18-month-old rats, we examined the ultrastructural and cytochemical features of multinucleated fibroblastic cells (MFCs) in the periodontal ligament (PDL) of molars. In aged rats, the MFCs were distributed randomly in the PDL and exhibited cytoplasmic structural variations which were not dependent on the number of nuclei. There was a tendency for the MFCs to cluster in the PDL. The MFCs, rich in cytoplasmic organelles involved with procollagen synthesis such as rough endoplasmic reticulum and the Golgi apparatus, incorporated and secreted 3H-proline-labelled products. The MFCs also possessed many phagosomes containing intact collagen fibrils. These MFCs were apparently involved in phagocytosis and intracellular degradation of incorporated collagen fibrils. Phagosome-rich MFCs contain acid phosphatase activity in primary and secondary lysosomes, similar or stronger in intensity to that which can be demonstrated in mononuclear fibroblasts. However, unlike mononuclear fibroblasts, the MFCs did not exhibit alkaline phosphatase activity along their plasma membranes. These results suggest that MFCs demonstrate a range of fibroblastic cellular activity, including collagen phagocytosis, and that they may lack certain plasma membrane glycoproteins, which might explain the occurrence of multinucleation in these cells.

Acid Phosphatase↗
PubMed1995

Differences in brain 5-HT transporter dissociation rates among animal species.

The potential of using receptor-ligand dissociation rates as a model for investigating molecular changes in receptors was tested using the dissociation of [3H]citalopram, [3H]paroxetine and [3H]imipramine from the brain 5-HT transporter of four different species (mouse, rat, pig and man). Since the dissociation rates of each of the three ligands differed in most of the species investigated, receptor-ligand dissociation rate constants would seem to be a sensitive measure of receptor conformation. The model could be useful in the search of structural variation in receptors whether attributable to genetic factors or to posttranslational modification.

Adrenergic Uptake Inhibitors↗
PubMed1987

Monoclonal antibodies reacting selectively with core and O-polysaccharide of Yersinia enterocolitica O:3 lipopolysaccharide.

In order to obtain specific tools for studying the alterations of the immunochemical structure of Yersinia enterocolitica lipopolysaccharide in various conditions, we have produced monoclonal antibodies reacting with core and O-polysaccharide chains of Yersinia enterocolitica O:3 LPS. Immunizations were made with whole bacterial cells and outer membrane preparation, respectively. Monoclonal antibody 2B5 reacted in enzyme immunoassay with purified core-lipid A complex, and its binding was not inhibited by Polymyxin B, suggesting that the target determinant is in the outer core. 2B5 recognized 100% of all tested Y. enterocolitica O:3 strains (n = 152) and reacted to some extent also with many other gram-negative bacteria. In immunoblotting with 2B5, a band corresponding to core-lipid A complex was visualized both with Y. enterocolitica, Brucella abortus and Haemophilus influenzae. In immunofluorescence assay, the only positive reaction was seen with Y. enterocolitica. Monoclonal antibody A6 reacted in enzyme immunoassay with purified O-polysaccharide chains, recognized 100% of tested Y. enterocolitica O:3 strains, and showed no cross-reactions with other bacteria. A typical ladder pattern was not seen in the immunoblotting analysis with A6. This suggests that the O-chain of Y. enterocolitica O:3 may be different from those in other gram-negative bacteria. These two antibodies will make it possible to study the structural variations of Yersinia enterocolitica LPS more precisely than described before, because of their fine specificity against important immunogenic components of LPS. They will also be useful in serology measuring the immune response against the target determinants of these antibodies.

Antibodies, Monoclonal↗
PubMed1999

Comparison of three different methods in monoclonal antibody-based detection of Streptococcus agalactiae protein serotype markers.

Surface-exposed proteins are important serotype markers in Streptococcus agalactiae (group B streptococci; GBS). The proteins include the c proteins c(alpha) and c(beta), the R4 protein and a protein provisionally called P. For all of these markers, protein-specific monoclonal antibodies (MAbs) have been generated. We have compared whole-cell-based fluorescent antibody testing (FAT), ELISA, and dot blotting for MAb-based detection of these proteins by testing a panel of 52 GBS isolates of different capsular antigen types. Of a total of 208 observations with each of the tests, positive signalling in the dot assay was observed in 32.2%, with ELISA in 27.8%, and with FAT in 26.4% of the recordings. Discordant results were noted most frequently with the c(beta) and c(alpha) MAbs. In the case of c(alpha) the reason for the discordant test results was further examined and it appeared that this could be attributed to low level expression of the c(alpha) protein, although structural variations of c(alpha) proteins cannot be excluded. Our findings favour dot blotting as the method of choice although we consider all three methods acceptable for serotyping of GBS.

Animals↗
PubMed2007

Curcumin and kolaviron ameliorate di-n-butylphthalate-induced testicular damage in rats.

The present study was carried out to evaluate the ameliorative effects of kolaviron (a biflavonoid from the seeds of Garcinia kola) and curcumin (from the rhizome, Curcuma longa L.) on the di-n-butylphthalate (DBP)-induced testicular damage in rats. Administration of DBP to rats at a dose of 2 g/kg for 9 days significantly decreased the relative testicular weights compared to the controls, while the weights of other organs remained unaffected. Curcumin or kolaviron did not affect all the organ weights of the animals. While only DBP treatment significantly increased the testicular malondialdehyde level and gamma-glutamyl transferase activity (gamma-GT), it markedly decreased glutathione level, the testicular catalase, glucose-6-phosphate dehydrogenase, superoxide dismutase, sperm gamma-GT activities and serum testosterone level compared to the control group. Data on cauda epididymal sperm count and live/dead ratio were not significantly affected in the DBP-treated rats. Alone, DBP treatment resulted in a 66% decrease in spermatozoa motility and a 77% increase in abnormal spermatozoa in comparison to control. DBP-treated rats showed marked degeneration of the seminiferous tubules with necrosis and defoliation of spermatocytes. The DBP-induced injuries in biochemical, spermatological parameters and histological structure of testis were recovered by treatment with kolaviron or curcumin. The pattern in the behaviour of these compounds might be correlated with their structural variations. Our results indicate that kolaviron and curcumin protect against testicular oxidative damage induced by DBP. The chemoprotective effects of these compounds may be due to their intrinsic antioxidant properties and as such may prove useful in combating phthalate-induced reproductive toxicity.

Animals↗
PubMed2006

Thrombin-like enzymes from venom gland of Deinagkistrodon acutus: cDNA cloning, mechanism of diversity and phylogenetic tree construction.

AIM: To clone cDNAs of thrombin-like enzymes (TLEs) from venom gland of Deinagkistrodon acutus and analyze the mechanisms by which their structural diversity arose. METHODS: Reverse transcription-polymerase chain reaction and gene cloning techniques were used, and the cloned sequences were analyzed by using bioinformatics tools. RESULTS: Novel cDNAs of snake venom TLEs were cloned. The possibilities of post-transcriptional recombination and horizontal gene transfer are discussed. A phylogenetic tree was constructed. CONCLUSION: The cDNAs of snake venom TLEs exhibit great diversification. There are several types of structural variations. These variations may be attributable to certain mechanisms including recombination.

Amino Acid Sequence↗
PubMed2026

Crawling under the radar: Two novel Paulinella species expand knowledge about the ecology and evolution of a primary plastid-containing amoeba lineage.

The genus Paulinella represents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae, Paulinella marae sp. nov. and Paulinella murrayi sp. nov., isolated from a brackish water habitat in North Carolina, United States. Complete chromatophore genomes and mitochondrial data revealed conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncovered significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosynthetic Paulinella species are globally distributed yet under-sampled. These results increase known species diversity within the clade from four to six and highlight the importance of integrating field-based observations with genomic approaches. Overall, this work advances Paulinella as a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low-abundance microbial eukaryotes.

Paulinella↗
PubMed2025

Chromatin accessibility analysis reveals functional cis-regulatory regions related to fruit development and domestication in tomato.

Non-coding DNA sequences harbor vast regulatory programs that ensure the precise spatiotemporal control of gene expression, which is essential for proper plant development and trait formation. Chromatin accessibility analysis could identify functional DNA regions within the extensive non-coding sequences and infer regulatory elements, serving as a crucial approach to unravel the mysteries of non-coding DNA sequences. Tomato fruit, a fleshy organ, provides a special system for studying fruit development and trait formation. However, the role of cis-accessible chromatin regions (cis-ACRs) during tomato fruit development, particularly in comparison with protein-coding DNA sequences, remains poorly understood. Here, we used ATAC-seq to define the landscape of cis-ACRs during fruit development and domestication in tomato. Temporal differential analysis revealed the dynamic opening and closing of cis-ACRs during fruit development. Comparative analysis of cis-ACRs between cultivated and wild tomatoes highlighted their significant contributions to fruit domestication. Combining analysis with genomic structural variations (SVs) suggested that SVs are likely a key factor in the formation of specific accessible cis-ACRs in cultivated tomatoes. Moreover, using gene editing, we identified a functional cis-ACR within the intron of the MBP3 gene that regulates fruit development and size traits. Overall, our findings provide a comprehensive perspective on the roles of cis-ACRs in tomato fruit development and domestication.

Solanum lycopersicum↗
PubMed2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Potato (Solanum tuberosum L.) is cultivated for its tubers, which serve as a major crop. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of flowering time, that functions as a tuberigen, the equivalent of a florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of the tetraploid potato cultivar, Atlantic. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129 218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

Solanum tuberosum↗
PubMed2026

Transposable elements as modulators of homoeologous gene expression in bread wheat: lessons from the pan-transcriptome era.

Bread wheat (Triticum aestivum L.) is an allohexaploid (AABBDD) whose three ancestral subgenomes generate complex patterns of gene regulation. Most genes exist as homoeologous triads, and the relative expression balance among copies, homoeolog expression bias, is central to polyploid evolution and adaptation. Recent high-quality assemblies, long-read transcriptomics, and pan-transcriptome resources have uncovered extensive cultivar-specific transcriptional diversity. Because transposable elements (TEs) compose over 80% of the wheat genome, they are prime candidates for shaping subgenome asymmetry. We synthesize recent pan-genomic and transcriptomic evidence, including genome-wide associations between TE insertions and genome-specific expression, and propose a unifying framework in which TEs modulate homoeolog expression by donating cis-regulatory sequences, altering chromatin states, producing small RNAs, and driving structural variation. We discuss experimental and computational challenges for establishing causality, and outline future functional and translational strategies to leverage TE-associated regulatory diversity in wheat breeding.

Triticum↗
PubMed2000

Staged growth of optimized arterial model trees.

There is a marked difference in the structure of the arterial tree between epi- and endocardial layers of the human heart. To model these structural variations, we developed an extension to the computational method of constrained constructive optimization (CCO). Within the framework of CCO, a model tree is represented as a dichotomously branching network of straight cylindrical tubes, with flow conditions governed by Poiseuille's law. The tree is grown by successively adding new terminal segments from randomly selected points within the perfusion volume while optimizing the geometric location and topological site of each new connection with respect to minimum intravascular volume. The proposed method of "staged growth" guides the generation of new terminal sites by means of an additional time-dependent boundary condition, thereby inducing a sequence of domains of vascular growth within the given perfusion volume. Model trees generated in this way are very similar to reality in their visual appearance and predict diameter ratios of parent and daughter segments, the distribution of symmetry, the transmural distribution of flow, the volume of large arteries, as well as the ratio of small arterial volume in subendocardial and subepicardial layers in good agreement with experimental data. From this study we conclude that the method of CCO combined with staged growth reproduces many characteristics of the different arterial branching patterns in the subendocardium and the subepicardium, which could not be obtained by applying the principle of minimum volume alone.

Algorithms↗
PubMed1984

Vitamin D3--resistant fibroblasts have immunoassayable 1,25-dihydroxyvitamin D3 receptors.

Cultured fibroblasts obtained from patients with tissue resistance to 1,25-dihydroxyvitamin D3 (vitamin D3--dependent rickets, type II) contain normal, low, or undetectable concentrations of this hormone's receptor protein as measured by a ligand-binding assay. Extracts from these cells were evaluated for receptors by immunoassay with a recently developed monoclonal antibody to the chick receptor. The results show that a protein sedimenting at 3.7S and recognizable by the antibody exists in comparable concentrations in cells from both normal and resistant patients, irrespective of the hormone-binding abnormalities of the cells. This implies that deficiencies in hormone binding associated with inherited tissue resistance to 1,25-dihydroxyvitamin D3 probably arise from structural variations in the receptor molecule and not from defective receptor synthesis.

Antibodies, Monoclonal↗
PubMed2002

Distribution of microbes producing antimicrobial epsilon-poly-L-lysine polymers in soil microflora determined by a novel method.

We developed a simple and sensitive screening method to investigate the distribution of microbes producing an antimicrobial poly(amino acid), epsilon-poly-L-lysine (epsilon-PL), in microflora. An acidic dye, Poly R-478, incorporated in an agar plate detected epsilon-PL producers by electrostatic interaction with the secreted basic polymers. All epsilon-PL producers, isolated after careful and sufficient screening of soil microflora, belonged exclusively to two groups of bacteria of the family Streptomycetaceae and ergot fungi. They were characterized based on the density and diameter of the concentric zone formed by the secreted polymers. The density depended on each isolate. The increase in the diameter of the concentric zone per unit of time varied among isolates and was negatively correlated with the molecular weight. Although the distribution of epsilon-PL producers was extremely limited, their products were structurally varied. The molecular masses of the secreted polymers among the isolates ranged from 0.8 to 2.0 kDa. There were also isolates producing unknown polymers inconsistent with the correlation or producing a mixture of polymers with original and modified structures. A chemically modified polymer was an epsilon-PL derivative, as determined by mass spectrometry. Since the structural variations had no relation to the phylogenetic position of the isolates, it is possible that enzymes involved in the synthesis diversified after putative horizontal transfers of relevant genes.

Bacteria↗