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PubMed1979

[Structural analysis of the capsules around breast prostheses (light and electron microscopic studies)].

Fibrous tissue capsules around silicone-gel and saline filled breast implants were examined by light microscopy as well as by transmission and scanning electron microscopy. This study revealed the following details: 1. Regularly arranged dense connective tissue forms the basis of the reactively developed capsules around the breast implants. This tissue contains bundles of collagenous fibers which are densely packed and lie parallel to each other forming structures of great tensile strengthes. 2. The outer surface of the connective tissue capsules contain reticulum fibers, the diameter of which is small. The fibers branch variously to form a netlike framework, which obviously can support the mechanical significance of the collagenous material. 3. At the inner surface fibrocytes and histiocytes are single layered and form an epithelium-like structure. These cells possess specializations of their free surface as microvilli, microplicae, and cell protrusions. In some areas dense connective tissue forms a felt-like surface. 4. Contractile fibroblasts (myofibroblasts) were found in these fibrous capsules. These cells share electron microscopic features of both smooth muscle cells and fibroblasts. Along with the rough endoplasmic reticulum and Golgi apparatus, these cells have long thin bundles of microfilaments. 5. The connective tissue of the capsules contains also capillaries and fibrocytes, which are usually deployed along bundles of collagen fibers and appear in sections as fusiform elements with long processes. The fibrocytes also contain lysosomes, and because these are involved in hydrolysis or digestion of material within the cell, their appearance depends upon their functional state, leading to their characteristic pleomorphism. 6. The frequently resulting unshapelyness of the breast implants cannot be caused by the action of the so-called myofibroblasts, the number of which is too small, but more likely because of the unelestic arrangement of large amounts of collagenous material.

Breast↗
PubMed1976

Structural analysis of O2'-methyl-5-carbamoylmethyluridine, a newly discovered constituent of yeast transfer RNA.

A compound tentatively identified as O2-methyl-5-carboxymethyluridine (cm5Um) was recently isolated in this laboratory from bulk yeast transfer RNA (Gray, M. W. (1975), Can, J. Biochem. 53, 735-746). Alkaline hydrolysis of yeast tRNA releases this nucleoside as part of an alkali-stable dinucleotide, cm5Um-Ap, from which sufficient cm5Um was prepared in the present investigation for a detailed examination of its properties. The ultraviolet absorption spectra and chromatographic and electrophoretic properties of cm5Um were consistent with the proposed structure, which was confirmed by characterization of the base and sugar moieties as 5-carboxymethyluracil and 2-O-methylribose, respectively. Snake venom hydrolysis of yeast tRNA releases cm5Um in the form of a carboxyl-blocked 5'-nucleotide, designated pU-2. Identification of the alkali-labile blocking group in pU-2 as an amide was based on quantitative assay for ammonia released upon acid hydrolysis of the corresponding nucleoside, U-2, and by chromatographic comparison of U-2 with the semisynthetic methyl ester and amide derivatives of cm5Um (mcm5Um and ncm5Um, respectively). Quantitative analysis has indicated that ncm5Um may be confined to a single species of yeast tRNA. In view of the unique localization (the "Wobble" position of the anticodon sequence) and coding properties (pairing with A but not with G) of other cm5U derivatives in transfer RNA, the dinucleotide cm5Um-Ap may be derived from the first two positions of the anticodon sequence of a yeast tRNA species recognizing an NUA codon. This predicts that O2-methyl-5-carbamoylmethyluridine will be found in an isoleucine, leucine, or valine isoacceptor.

Ammonia↗
PubMed2026

Deep generative models in biological sequence and structure analysis and design.

Deep generative models have transformed biological sequence modeling from predictive analysis toward increasingly controllable design. Early biological applications of Variational Autoencoders (VAEs) and Generative Adversarial Networks (GANs) established latent representation learning and sequence synthesis, while recent advances in transformer-based language models, discrete diffusion, flow-matching, and multimodal generative frameworks have substantially expanded the scope of biological design. This review examines generative models for DNA, RNA, and protein sequence design, emphasizing how different model classes represent biological constraints, operate over discrete and continuous spaces, and integrate sequence, structure, and function. We compare VAEs, GANs, autoregressive and masked language models, diffusion models, and flow-based approaches across genomics, transcriptomics, and proteomics, with particular attention to controllability, long-range dependency modeling, structural grounding, generalization, and experimental utility. We further examine evaluation strategies, out-of-distribution generalization, and closed-loop design-build-test-learn workflows that connect in silico generation with empirical validation. We distinguish fundamental modality-dependent constraints including sequence discreteness, context length, structural coupling, and physical or thermodynamic requirements from architecture-dependent advantages that reflect the current state of the field. Current studies suggest that long-context models are particularly useful for genome-scale representation and sequence modeling, whereas structure-aware diffusion, flow-based, and inverse-folding approaches provide better frameworks for geometry-constrained RNA and protein design. This perspective provides a critical framework for understanding the present capabilities, limitations, and convergence of generative approaches toward reliable and experimentally grounded biological design.

Biological sequence analysis↗
PubMed1977

Purification and structural analysis of the fourth component of human complement.

The fourth component of human complement (C4) has been purified in 20% yield from fresh plasma using as starting material the 5-12% poly(ethylene glycol) precipitate which had been depleted of plasminogen by an affinity adsorbent. Sequential ion-exchange chromatography on diethylaminoethylcellulose, QAE-Sephadex, and DEAE-Bio-Gel A resulted in C4 homogeneous by immunological criteria and by polyacrylamide gel electrophoresis, the last chromatographic step achieving separation of native from inactivated C4. Reduction with 20 mM dithiothreitol for 2 h at 37 degrees C in 0.25 M 2-amino-2-hydroxymethyl-1,3-propanediol hydrochloride, pH 8.6, effected cleavage of the interchain disulfide bonds. A three-chain structure for C4 was confirmed, and molecular weight estimates of 93 000 +/- 9300, 75 000 +/- 7500, and 30 000 +/- 3000 determined for the alpha, beta, and gamma chains, respectively. The effects of known inactivators of C4 upon the chains of C4 were investigated, confirming that the inactivations by C1s and trypsin were accompanied by the fragmentation of the alpha chain. Inactivation of C4 by hydrazine, on the other hand, produced no detectable change in chain size. Separation of the chains was accomplished by gel filtration in the presence of 1 M acetic acid. Amino acid compositions of native C4 and the constitutive chains have been performed, and N-terminal sequences of the latter established by automated Edman degradation.

Amino Acid Sequence↗
PubMed1977

Structural analysis of human neutrophil migration. Centriole, microtubule, and microfilament orientation and function during chemotaxis.

Orientation of nucleus, centriole, microtubules, and microfilaments within human neutrophils in a gradient of chemoattractant (5 percent Escherichia coli endotoxin-activated serum) was evaluated by electron microscopy. Purified neutropils (hypaque-Ficoll) were placed in the upper compartment of chemotactic chambers. Use of small pore (0.45 mum) micropore filters permitted pseudopod penetration, but impeded migration. Under conditions of chemotaxis with activated serum beneath the filter, the neutrophil population oriented at the filter surface with nuclei located away from the stimulus, centrioles and associated radial array of microtubules beneath the nuclei, and microfilament-rich pseudopods penetrating the filter pores. Reversal of the direction of the gradient of the stimulus (activated serum above cells) resulted in a reorientation of internal structure which preceded pseudopod formation toward the activated serum and migration off the filter. Coordinated orientation of the entire neutrophil population did not occur in buffer (random migration) or in a uniform concentration of activated serum (activated random migration). Conditions of activated random migration resulted in increased numbers of cells with locomotory morphology, i.e. cellular asymmetry with linear alignment of nucleus, centriole, microtubule array, and pseudopods. Thus, activated serum increased the number of neutrophils exhibiting locomotory morphology, and a gradient of activated serum induced the alignment of neutrophils such that this locomotory morphology was uniform in the observed neutrophil populayion. In related studies, cytochalasin B and colchicines were used to explore the role of microfilaments and microtubules in the neutrophil orientation and migration response to activated serum. Cytochalasin B (3.0 mug/ml) prevented migration and decreased the microfilaments seen, but allowed normal orientation of neutrophil structures. In an activated serum gradient, colchicines, but not lumicolchicine, decreased the orientation of nuclei and centrioles, and caused a decrease in centriole-associated microtubules in concentrations as low as 10(-8) to 10(-7) M. These colchicines effects were associated with the rounding of cells and impairment of pseudopod formation. The impaired pseudopod formation was characterized by an inability to form pseudopods in the absence of a solid substrate, a formation of narrow pseudopods within a substrate, and a defect in pseudopod orientation in an activated serum gradient. Functional studies of migration showed that colchicines, but not lumicolchicine, minimally decreased activated random migration and markedly inhibited directed migration, but had not effect on random migration. These studies show that, although functioning microfilaments are probably necessary for neutrophil migration, intact microtubules are essential for normal pseudopod formation and orientation, and maximal unidirectional migration during chemotaxis.

Blood↗
PubMed1979

Structural analysis of precursor and product forms of type-common envelope glycoprotein D (CP-1 antigen) of herpes simplex virus type 1.

The type-common CP-1 antigen of herpes simplex virus type 1 (HSV-1) is associated in the infected cell with two components, a 52,000-molecular-weight glycoprotein (gp52 or pD) and a 59,000-molecular-weight glycoprotein (gp59 or D). The larger form (D) is also found in the virion envelope. It was postulated that pD is a precursor of D. We found that pD shared methionine and arginine tryptic peptides with D isolated from infected cell extracts. D isolated from infected extracts had the same trypric methionine peptide profile as D isolated from the virion envelope. Thus, processing of pD to D does not involve any major alterations in polypeptide structure. Furthermore, D did not share tryptic methionine peptides with the other major glycoproteins of HSV-1. Using [2-3H]mannose as a specific glycoprotein label, we found that pD, which is a basic protein (isoelectric point = 8.0) contained a 1,800-molecular-weight oligomannosyl core moiety and was processed by further glycosylation and sialyation to a more acidic and heterogeneous molecule D, which as a molecular weight of at least 59,000.

Antigens, Viral↗
PubMed2026

Genomic and structural analysis of dacB variants associated with cephalosporin resistance in Pseudomonas aeruginosa.

The rise of resistance to fourth-generation cephalosporin in Pseudomonas aeruginosa (P. aeruginosa) is a global concern. The resistance is largely driven by variants of chromosomally encoded AmpC β-lactamase, known as Pseudomonas-derived cephalosporinase (PDC), which arise from the mutations in the ampC gene. In addition, alteration in dacB, which encode the penicillin-binding protein 4 (PBP4), can lead to the overexpression of ampC, thereby contributing to β-lactam resistance. Present work analyzed 208 clinical isolates of P. aeruginosa using whole-genome sequencing (WGS) and detected multiple nonsynonymous single nucleotide polymorphisms (nsSNPs), such as Y264C, G444D, and a double mutation (A394P-T428P). All nsSNPs were predicted to be deleterious by several prediction program. Molecular dynamics (MD) simulations suggested that these substitutions destabilize PBP4, increase structural flexibility, and contribute to the resistance mechanism, which favored their selection. To determine the effective therapeutics against these mutations, molecular docking was conducted with various antibiotics. Cefoperazone exhibited the highest binding affinity (-7.3 kcal/mol) among multiple PBP4 variants. The Molecular dynamics (MD) simulations and Molecular Mechanics Poisson Boltzmann Surface Area calculations (MMPBSA) further confirmed the favorable interactions between cefoperazone and PBP4 variants. In vitro MIC analyses supported these findings, indicating that cefoperazone displayed significant activity against clinical dacB mutants of P. aeruginosa. The study offers structural insight of dacB variants leading to antibiotic resistance and emphasizes the need to prioritize specific antibiotics to address the challenges arising from protein mutations.

Pseudomonas aeruginosa↗
PubMed1977

Structural analysis of the molecular evolution of some gastro-entero-pancreatic hormones.

By means of a statistical analysis of the occurrence of amino-acid residues in the polypeptide chains of several gastro-entero-pancreatic (GEP) hormones an investigation was undertaken to determine whether any of these hormones might be related to each other--possibly from an evolutionary point of view. Particular interest was paid to the occurrence of small charged segments, i.e. those with acidic or basic amino acid residues, since such segments can be presumed to play a role in hormonal receptor binding mechanisms. By this method hormonal relationships were suggested by the observation that these small charged amino-acid sequences, contained in the hormonal structures, match as a result of non-randomness. It was found that hagfish and human insulin were related on a molecular level not only to the newly discovered (avian, bovine, human) pancreatic polypeptide (PP) but also to some other GEP hormones (VIP, GIP, glucagon) as well as to calcitonin and to the alpha-subunit of the glycoprotein hormones. Interpretation of the statistical data suggests that all these peptide hormones are related by a common hexapeptide sequence which contributed, at an evolutionary point, to their molecular architecture. A hexapeptide segment of APP is statistically related to a sequence of equal size in the carboxy terminal region of the A-chain of both hagfish and human insulin, providing the first instance of their structural similarity. Correlations between PP, insulin, glucagon, VIP, and calcitonin provide a tentative basis for predicting the production of one or more of these peptide hormones by immature or de-differentiated cells of neoplasms and non-neoplastic pathologic lesions of the GEP endocrine system.

Amino Acid Sequence↗
PubMed1979

Structural analysis of the intracellular RNAs of murine mammary tumor virus.

We have characterized murine mammary tumor virus (MuMTV)-specific RNA in several types of cells in which viral DNA is transcribed into RNA: cultured GR mouse mammary tumor cells, S49 lymphoma cells from BALB/c mice, lactating mammary glands from C57BL/6 mice, and mink lung cells infected in vitro with MuMTV. In all cell types studied, there are three distinct species of intracellular viral RNA, with sedimentation coefficients of 35S, 24S, and 13S (or molecular weights of 3.1 X 10(6), 1.5 X 10(6), and 0.37 X 10(6), as determined by rate-zonal sedimentation in sucrose gradients and by electrophoresis in agarose gels under denaturing conditions. These three viral RNA species appear to be present regardless of viral RNA concentration, responsiveness to glucocorticoid hormones, production of extracellular virus, and use of either endogenous or acquired MuMTV proviral DNA as template. The three viral RNAs display characteristics of mRNAs in that they are polyadenylated, associated with polyribosomes, and released from polyribosomes by treatment with EDTA; hence all three species presumably direct the synthesis of virus-coded proteins. The two larger species of viral RNA are probably responsible for synthesis of the structural proteins of the virion, but the function of the 13S RNA is not known. Both of the subgenomic RNAs contain sequences found at the 3' terminus of 35S (or genomic) RNA. However, only the 24S RNA (not the 13S RNA) contains sequences which are located at the 5' terminus of 35S RNA and are apparently transposed during RNA synthesis of maturation, as described for subgenomic mRNA's of other retroviruses.

Base Sequence↗
PubMed1979

Organ culture of adult amphibian heart: a fine structural analysis.

Pieces of hearts from adult newts were cultured up to 2 months. Within 7 days of culture, approximately 37% of the cardiac explants were attached to the substrate and more than 33% of the attached explants and approximately 15% of the unattached explants established pulsation rates ranging from 3 to 67 beats/min. The control and cultured explants were processed at weekly intervals for electron microscopy. The diameter of the control cardiac muscle cells ranged approximately 3-5 micron. The cell surface was provided with microvilli. The intercellular spaces ranged approximately 150-500 A. The intercalated discs lacked the step-like courses observed in the mammalian cardiac muscle. Sarcoplasmic reticulum was scanty. Desmosomal-dense materials were frequently continuous with the Z-bands of both control and cultured cardiac muscle cells. The transverse tubular system and gap junction were absent in newt ventricles. The functional implications of these characterisitics are discussed. At the end of 1 week of culture, the surfaces of the explants were covered by one or more layers of non-muscle cells, and the core of the explants consisted mostly of cardiac muscle cells. In a few cardiac muscle cells the myofibrillar organization was disrupted, resulting in the distribution of scattered patches of myofibrils and free myofilaments in the sarcoplasm. A small number of intact muscle cells contained a considerable number of dense granules in the sarcoplasm. At 15 days in culture, a large number of muscle cells showed structural features reminiscent of embryonic cardiac muscle cells. These cells possessed patches of myofibrils, scattered myofilaments and scanty sarcoplasmic reticulum along with other cellular organelles and inclusions. Several of these altered cardiac muscle cells contained mitotic figures. The cardiac explants maintained the initial beating rate until the end of 2 months of culture, except for the 11% of the explants which stopped beating. By 3-4 weeks in culture, most of the cardiac muscle cells possessed the altered cell morphology mentioned above. The explants after 60 days in culture became more flattened than the earlier explants. The intact cardiac muscle cells were rare, and the cores of the explants were mostly occupied by the altered cardiac muscle cells. It is evident from our studies that the cardiac muscle cells have undergone dedifferentiation in long-term culture, and that this dedifferentiation process has yet had no effect in the maintenance of contractility of the explants. Furthermore, these dedifferentiated cardiac muscle cells are capable of DNA synthesis and mitosis.

Animals↗
PubMed1979

Structural analysis of the fibroin gene at the 5' end and its surrounding regions.

Using the genomic clones of the fibroin gene with its flanking sequences, a detailed restriction map was prepared with particular attention given to the region neighboring the 5' end of the gene. About 60% of the fibroin mRNA has a complete cap (m7GpppAmUmCXG), and the remaining 40% has an unmethylated cap (GpppAPyXXG). The latter can be radioactively labeled by the use of vaccinia capping enzymes. Using the labeled mRNA, we mapped the 5' end of the gene by hybridization to restriction enzyme digests. DNA sequencing of this region revealed a sequence ATCAGCATCAG that corresponds to ApyXXG in tandem. The 5' end of mRNA with a complete cap was also located in these 11 nucleotides. Since the second ATCAG region was protected from S1 digestion following hybridization with total fibroin mRNA, we have tentatively assigned it as the sole 5' end of the transcription unit. About 700 bp were sequenced in the region from -800 + 1700 bp. The region of about 210 bp preceding the 5' end of the gene which may accommodate a promoter sequence is very AT-rich and contains clusters of A and T residues. This region contains statistically significant dyad symmetries, direct repeats and inverted repeats. At -30 to -24, the sequence TATAAAA was observed, and this is similar to a Pribnow-type sequence (TATAGATG). The sequence that codes for the gly-ala repetitious peptide characteristic of fibroin begins somewhere between 1340 and 1600 bp from the 5' end. An intervening sequence of about 1.1 kb that interrupts the gene about 70 bp from the 5' end was detected by R loop formation. Structures of the fibroin gene cloned from fibroin producing and nonproducing cells look the same, especially around the 5' end and the intervening region.

Animals↗
PubMed1978

Structural analysis of viral replicative intermediates isolated from adenovirus type 2-infected HeLa cell nuclei.

Deoxyribonucleoprotein complexes released 17 h postinfection from adenovirus type 1 (Ad2)-infected HeLa cell nuclei were shown by electron microscopy to contain filaments much thicker (about 200 A [20 nm]) than double-stranded DNA (about 20 A [2 nm]). The complexes were partially purified through a linear sucrose gradient, concentrated, and further purified in a metrizamide gradient. The major protein present in the complexes was identified as the 72,000-dalton (72K), adenovirus-coded single-stranded DNA-binding protein (72K DBP). Three types of complexes have been visualized by electron microscopy. Some linear complexes were uniformly thick, and their length corresponded roughly to that of the adenovirus genome. Other linear genome-length complexes appeared to consist of a thick filament connected to a thinner filament with the diameter of double-stranded DNA. Forked complexes consisting of one thick filament connected to a genome-length, thinner double-stranded DNA filament were also visualized. Both thick and thin filaments were sensitive to DNase and not to RNase, but only the thick filaments were digested by the single-strand-specific Neurospora crassa nuclease, indicating that they correspond to a complex of 72K DBP and Ad2 single-stranded DNA. Experiments with anti-72K DBP immunoglobulins indicated that these nucleoprotein complexes, containing the 72K DBP, correspond to replicative intermediates. Both strands of the Ad2 genome were found associated to the 72K DBP. Altogether, our results establish the in vivo association of the 72K DBP with adenovirus single-stranded DNA, as previously suggested from in vitro studies, and support a strand displacement mechanism for Ad2 DNA replication, in which both strands can be displaced. In addition, our results indicate that, late in infection, histones are not bound to adenovirus DNA in the form of a nucleosomal chromatine-like structure.

Adenoviruses, Human↗
PubMed1979

Structural analysis of functionally different smooth muscles.

The ultrastructure of the longitudinal and circular muscle cells of the guinea pig stomach which show different contractile responses was compared. The extracellular space within the muscle bundles is about 12.1% in the longitudinal layer and about 4.4% in the circular layer. Nexuses were sonsistently found in the circular muscle layer but not in the longitudinal muscle layer. Numbers of both mitochondria and microtubules per unit area of smooth muscle cell are larger in the longitudinal than in the circular muscle. Cellular area occupied by sarcoplasmic reticulum is about 4.7% in the longitudinal muscle, 2.3% in the circular muscle. The numbers of caveolae are almost the same in both tissues. The most distinct difference between the two types of smooth muscle is the appearance of the thick filaments. The circular muscle cell contains approximately 50 thick filaments per 0.5 micron 2 of cytoplasmic area, while the longitudinal muscle cell only about 25 filaments which were usually much thinner than those of the circular muscle. These results indicate that the contractile apparatus itself is different in longitudinal and circular smooth muscles of the guinea pig stomach.

Animals↗