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PubMed1987

Sugar interaction with biologically active cis-PtCl2(NH3)2 (anticancer) and its inactive trans isomer.

The interaction of D-glucuronic and D-gluconic acids with cis- and trans-PtCl2(NH3)2 (cisplatin and transplatin) has been investigated in aqueous solution and solid complexes of the type cis-[PtL(NH3)2]L.H2O and trans-[PtL2(NH3)2]L.H2O, where L = D-glucuronate or D-gluconate anions, are isolated and characterized by means of Fourier transform-infrared and 1H-NMR spectroscopy, and molar conductivity and X-ray powder diffraction measurements. Spectroscopic and other evidence indicated that the sugar anions bind monodentately in trans-[PtL2(NH3)2].H2O and bidentately in cis-[PtL(NH3)2]L.H2O complexes through the carboxylate oxygen atoms and other sugar donor groups. The strong sugar intermolecular hydrogen-bonding network is altered to that of the sugar-OH...NH3(H2O)...OH-sugar, upon platinum-ammine interaction. The D-glucuronate anion has the beta-anomer configuration both in the free salt and in these platinum-sugar complexes.

Cisplatin↗
PubMed1981

Regional distribution of substance P-like immunoreactivity in the frog brain and spinal cord: immunohistochemical analysis.

With the indirect immunofluorescence technique of Coons, the overall distribution of the substance P (SP)-positive neuron system in the frog brain and spinal cord was explored. SP-positive cells were observed in more than ten areas, such as olfactory bulb, amygdaloid complex, septal area, bed nucleus of hippocampal commissure, hypothalamic periventricular zone, dorsal and ventral thalamus, infundibulum, torus semicircularis, optic tectum, the area dorsal to the interpeduncular nucleus, central gray matter of the mesorhombencephalon, and raphe region, etc. A dense network of SP-positive fibers was also widely distributed in the frog brain and spinal cord. SP-positive fibers were roughly divided into two types. One consisted of very fine SP-positive fibers and gave the region a diffuse appearance. The area medial to n. Bellonci, interpeduncular nucleus, n. isthmi, and optic tectum contained this type of SP-positive fibers. The other one consisted of clearly distinguishable varicose fibers. A number of SP-positive fibers located in the amygdaloid complex, striatal complex, hypothalamus, central gray matter of the mesorhombencephalon, trigeminal spinal nucleus, and posterior horn of the spinal cord belonged to this category. The functional role of the SP-positive neuron system in the central nervous system is also briefly discussed.

Animals↗
PubMed1991

Studies on the density, distribution, and surface phenotype of intraepithelial class II major histocompatibility complex antigen (Ia)-bearing dendritic cells (DC) in the conducting airways.

Conventional immunohistochemical analysis of airway intraepithelial class II major histocompatibility complex (Ia) expression demonstrates a morphologically heterogeneous pattern of staining, suggestive of the presence of a mixed population of endogenous antigen presenting cells. Employing a novel tissue sectioning technique in conjunction with optimal surface antigen fixation, we now demonstrate that virtually all intraepithelial Ia staining throughout the respiratory tree in the normal rat, can be accounted for by a network of cells with classical dendritic cell (DC) morphology. The density of DC varies from 600-800 per mm2 epithelial surface in the large airways, to 75 per mm2 in the epithelium of the small airways of the peripheral lung. All the airway DC costain for CD4, with low-moderate expression of a variety of other leukocyte surface markers. Both chronic (eosinophilic) inflammation and acute (neutrophilic) inflammation, caused respectively by inhalation of chemical irritants in dust or aerosolised bacterial lipopolysaccharide (LPS), are shown to be accompanied by increased intraepithelial DC density in the large airways (in the order of 50%) and up to threefold increased expression of activation markers, including the beta chain of CD11/18. The kinetics of the changes in the DC network in response to LPS mirrored those of the transient neutrophil influx, suggesting that airway intraepithelial DC constitute a dynamic population which is rapidly upregulated in response to local inflammation. These findings have important theoretical implications for research on T cell activation in the context of allergic and infectious diseases in the respiratory tract.

Animals↗
PubMed1990

Graph-set analysis of hydrogen-bond patterns in organic crystals.

A method is presented based on graph theory for categorizing hydrogen-bond motifs in such a way that complex hydrogen-bond patterns can be disentangled, or decoded, systematically and consistently. This method is based on viewing hydrogen-bond patterns topologically as if they were intertwined nets with molecules as the nodes and hydrogen bonds as the lines. Surprisingly, very few parameters are needed to define the hydrogen-bond motifs comprising these networks. The methods for making these assignments, and examples of their chemical utility are given.

Chemical Phenomena↗
PubMed2026

Molecular-networking-based characterization of cytotoxic metabolites produced by the cyanobacterium Nostoc edaphicum CCNP1411.

Cyanobacteria of the genus Nostoc, known for their large genomes and rich repertoire of biosynthetic gene clusters, represent a prolific source of structurally diverse secondary metabolites with diverse biological activities, including cytotoxic effects. However, the identification of bioactive compounds is often hindered by low metabolite abundance and difficulties in isolating sufficient quantities for individual testing. In this study, we investigated the cytotoxic potential of chromatographic fractions obtained from Nostoc edaphicum CCNP1411 using a combination of bioassay-guided fractionation and LC-MS/MS-based feature-based molecular networking (FBMN). Cytotoxic activity was evaluated using the MTT assay across a panel of epithelial and neuronal cancer cell lines, as well as normal human dermal fibroblasts. The most active fractions, eluted with 80-90% MeOH, exhibited broad cytotoxic effects across all tested cancer cell lines. Molecular networking analysis revealed that these fractions were dominated by lipid derivatives, including lysophospholipids, monoacylglycerols, and free fatty acids, whereas previously described peptide metabolites were distributed across all fractions and were unlikely to be the main agents responsible for the observed activity. Targeted testing of selected commercially available lipid compounds confirmed their cytotoxic effects, with lysophospholipids showing the highest potency in selected cell lines. However, dose-response analysis indicated that most compounds exhibited limited potency at lower concentrations, as reflected by relatively high IC₅₀ values. Overall, our results demonstrate that lipid constituents, previously overlooked as bioactive metabolites produced by N. edaphicum CCNP1411, contribute significantly to the cytotoxic activity of the tested fractions. The application of molecular networking enabled the prioritization of bioactive metabolites and highlights its utility in linking chemical composition with biological effects in complex cyanobacterial extracts.

Bioactivity-guided fractionation↗
PubMed1988

Production of IL-1-mimicking anti-idiotypic antibodies in rabbits in response to IL-1 immunization.

This report describes the characterization of immunoglobulins with interleukin-1 (IL-1)-like activity from the serum of rabbits immunized with partially purified mouse IL-1. Early after immunization, immune sera were found to contain anti-IL-1 antibodies (idiotypes) that inhibited IL-1 bioactivity (augmented-proliferation of PHA-stimulated thymocytes). Later, anti-idiotypic antibodies appeared that mimicked IL-1 activity. These IL-1-like antibodies were affinity purified either on an anti-IL-1-enriched Ig-Sepharose 4B column from an early bleed or sequentially on anti-Ig and Protein A immunoadsorbent columns. By ELISA anti-idiotypic antibodies specifically bound to rabbit anti-IL-1 antibodies. Functionally, IL-1 mimicking antibodies were reproducibly effective in augmenting the in vitro proliferation of PHA-stimulated thymocytes or Con A-stimulated D10 cells. On the other hand, they did not support proliferation of the IL-2-dependent CTLL-2 cells. The ability of IL-1-mimicking antibodies to enhance thymocyte proliferation could be blocked by functional site related anti-IL-1 antibodies. By Western blot, 125I-labeled IL-1 and IL-1-mimicking antibodies bound to a similar 23 Kd mol. wt protein material recovered from the lysate of thymocytes stimulated with PHA for 48 h. That the observed bioactivity could be attributed to antibody molecules and not to contaminant IL-1 was ascertained by several methods, namely (1) SDS-PAGE analysis of 125I-labeled material and (2) resistance to loss of bioactivity by lyophilization. Furthermore, as neither Ig-anti-Ig nor BSA-anti-BSA complexes mimicked IL-1-augmented thymocyte proliferation, a non-specific effect due to immune complexes could be excluded. The occurrence of antibodies mimicking several of the IL-1 functions induced following IL-1 immunization suggests a potential role for the idiotypic network in modulating cytokine activities and a possible link between regulation of the immune system by cytokines and immunoglobulin idiotypes.

Animals↗
PubMed1979

Comparative ultrastructure of Mycobacterium leprae and Mycobacterium lepraemurium cell envelopes.

The structural properties of the cell envelopes of Mycobacterium leprae and Mycobacterium lepraemurium were investigated by freeze-fracture, freeze-etching, and negative-staining techniques. Freeze-fracture split the cell wall and exposed the internal features of the peptidoglycolipid mycosidic filamentous network. The cell membrane was also split into two asymmetric faces. The external fracture face was characterized by linear arrays of intramembranous particles, whereas the protoplasmic fracture face showed randomly distributed clusters of particulate entities. Comparative analysis of the ultrastructural features observed in M. leprae and M. lepraemurium indicated that the organization of the cell envelope in these two species differed particularly with respect to the amount and complexity of the superficial peptidoglycolipid and mycosidic integument, which is poorly developed in the mycobacterium responsible for human disease.

Animals↗
PubMed2025

APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19.

MOTIVATION: Computational analyses of bulk and single-cell omics provide translational insights into complex diseases, such as COVID-19, by revealing molecules, cellular phenotypes, and signalling patterns that contribute to unfavourable clinical outcomes. Current in silico approaches dovetail differential abundance, biostatistics, and machine learning, but often overlook nonlinear proteomic dynamics, like post-translational modifications, and provide limited biological interpretability beyond feature ranking. RESULTS: We introduce APNet, a novel computational pipeline that combines differential activity analysis based on SJARACNe co-expression networks with PASNet, a biologically informed sparse deep learning model, to perform explainable predictions for COVID-19 severity. The APNet driver-pathway network ingests SJARACNe co-regulation and classification weights to aid result interpretation and hypothesis generation. APNet outperforms alternative models in patient classification across three COVID-19 proteomic datasets, identifying predictive drivers and pathways, including some confirmed in single-cell omics and highlighting under-explored biomarker circuitries in COVID-19. AVAILABILITY AND IMPLEMENTATION: APNet's R, Python scripts, and Cytoscape methodologies are available at https://github.com/BiodataAnalysisGroup/APNet.

COVID-19↗
PubMed1986

Evidence for the existence in the nuclei of Friend cells of a new type of ribonucleoprotein network.

We have isolated fragments of a novel nuclear structure exhibiting the morphological and biochemical characteristics of a ribonucleoprotein network. Under transmission electron microscopy it is visualized as irregularly interconnected branches assembled by tightly packed particles with sizes between 100A and 300A. RNA extracted from this structure shows a complex pattern: as well as ribosomal 28 S and 18 S RNA, small amounts of heterogeneous nuclear RNA and small nuclear RNA are also present. The protein composition of the network indicates a strong domination of ribosomal polypeptides. This fact, considered together with the sedimentation characteristics of the prevailing type of particles isolated directly from the network, supports the conclusion that ribosomal particles are the representative particulate elements. Further electrophoretic analysis of the protein has pointed out that it also contains a significant number of acidic polypeptides. Control experiments have suggested that the site of origin of the network fragments studied is not nucleolar: the fragments are released during extraction, most probably from the nuclear periphery. It is not yet clear whether this structure is localized only at the nuclear periphery or represents an extensive structure, occupying the entire volume of the nucleus. It is speculated that the network is involved in the extranucleolar transport and maturation of ribosomes.

Autoradiography↗
PubMedDate not supplied

Microencapsulation of pheromone-analogue and measurement of the sustained release.

A model study was conducted to establish 2 feasible production and application systems for the long-term, sustained release of pheromone into the atmosphere of targeted areas. The desired goal of effective release was set at least half a year. 2-Ethylhexyl acetate (EHA) was selected as a pheromone analogue due to its similar structure and easier access for quantitative analysis. At first EHA was impregnated in wax particles, which were then encapsulated employing the complex coacervation of a gelatin-gum arabic system. The release period of EHA through the gelatin wall, however, turned out to be too short--only a week at most. As a second attempt, a modification of the two-phase emulsion technique was employed to encapsulate multiple numbers of wax particles in hydrated networks of gelatin. Though the initial release rate of EHA was still too high, 60 per cent of encapsulated EHA underwent sustained release over six months after absorbed moisture had completely evaporated. A two-step mechanism of mass transfer was proposed and the related parameters in terms of the capacity coefficient and effective diffusion coefficient were estimated.

Acetates↗
PubMed1980

Identification of Ia on a subpopulation of human T lymphocytes that stimulate in a mixed lymphocyte reaction.

The delineation of discrete subpopulations of human T lymphocytes has permitted preliminary analyses of the complex cellular network regulating the immune response in man. We previously showed that a subset of T lymphocytes, designated as theophylline-sensitive because of their inability to bind sheep red blood cells in the presence of the drug, are responsible for antigen-specific suppression or regulation in an in vitro plaque-forming cell assay. We now show that 25 to 45% of these theophylline-sensitive T cells were Ia-positive by immunofluorescence with a rabbit antiserum raised against purified B lymphoblast surface antigenic material. These data suggested that 4 to 7% of peripheral blood T cells carry Ia determinants. The presence of Ia determinants on this T cell subset was confirmed by gel analysis of radioiodinated surface material. Furthermore, in mixed lymphocyte culture, the theophylline-sensitive cells demonstrated HLA-D determinants and were 10-fold more potent stimulators than equal numbers of B lymphocytes. The presence of Ia determinants on these T cells indicates the expression of major histocompatibility complex-related regulatory gene products on a specific human T lymphocyte subpopulation.

Animals↗
PubMed1985

Analysis of the morphology and function of primary cilia in connective tissues: a cellular cybernetic probe?

More than 300 primary cilia have been identified electronmicroscopically in a variety of embryonic and mature connective tissue cells. To further define the enigmatic function of these cilia, we examined the interrelationships between the basal apparatus and cytoplasmic organelles and the ciliary shaft and the extracellular matrix. The basal diplosome was consistently associated with the secretory organelles including the maturing face of the Golgi complex, Golgi vacuoles and vesicles, the microtubular network, the plasma membrane, and coated pits and vesicles. Small vesicles and amorphous granules were also observed within the ciliary lumen and adjacent to the ciliary membrane. Microtubule-membrane bridges linked axonemal tubules to the ciliary membrane. The position, projection, and orientation of the axoneme were influenced by the structural organisation and mechanical properties of the matrix and frequently caused angulation of the ciliary shaft relative to the basal body. Located midway between the secretory apparatus and the extracellular matrix, primary cilia would appear ideally situated to mediate the necessary interaction between the cell and its surrounding environment prerequisite to the formation and maintenance of a functionally effective matrix. We propose that primary cilia in connective tissue cells could act as multifunctional, cellular cybernetic probes, receiving, transducing, and conducting a variety of extrinsic stimuli to the intracellular organelles responsible for effecting the appropriate homeostatic feedback response to changes in the extracellular micro-environment.

Animals↗
PubMed1992

Structure and binding properties of a monoclonal anti-idiotypic autoantibody to anti-DNA with epibody activity.

We report the isolation and characterization of a mouse autoanti-idiotypic mAb (D7.4 IgG2a), which is directed against a major public Id (A52 IgG2b) in the murine and human autoimmune response to DNA. The natural anti-Id mAb has been produced in the course of the SLE-like disease in a female NZB/NZW F1 mouse and showed a dual specificity (epibody activity) for the public Id (A52) and for the autoantigen (DNA). The two binding activities were shown to reside in the Fab portion of the epibody and were highly specific for their respective Ag. A complete nucleotide sequence analysis of the D7.4 H and L chain V-region genes combined with computer comparisons to available Ig sequences may suggest a charge interaction between the H chain CDR3 segments of the Id and anti-Id antibodies. The D7.4 epibody may be a component of the self-binding, idiotypically connected network of natural antibodies. Alternatively, it could be elicited against the potentially pathogenic, DNA-containing immune complexes in order to facilitate their removal from the circulation of diseased individuals.

Amino Acid Sequence↗
PubMed1985

Structure and composition of synaptonemal complexes, isolated from rat spermatocytes.

Synaptonemal complexes (SCs) (structures involved in chromosome pairing during meiosis) were isolated and purified from rat spermatocytes for the purpose of biochemical and morphological analysis. Spermatocytes were lysed in a medium, containing Triton X-100, EDTA and DTT; the resulting swollen nuclei were disrupted by DNAse II, and the suspension was centrifuged through 1.5 M sucrose. The resulting preparation consisted for at least 60% of free SCs, as judged from electron micrographs of agar filtrates. The purified SCs still possessed lateral and transversal elements and attachment plaques. A small fraction also contained a central element. Particularly in diplotene SCs, the lateral elements clearly consisted of two subelements, which are connected by thinner fibres. The lateral elements may fall apart into a network of thinner fibres, presumably as a result of degradation during isolation. On SDS-polyacrylamide gels, the major protein components of purified SCs had relative mobilities (Mrs) of 67 to 60 and 57 to 55 kDa; in addition, there were minor proteins with Mrs of 90, 35, 33, 28, and 26 kDa, and varying amounts of histones. The 67 to 60 kDa proteins comigrate with lamins of rat liver pore complexes and laminae. A possible relationship between SCs and pore complexes and laminae is discussed.

Animals↗
PubMed1991

Multilocus genetic structure of ancestral Spanish and colonial Californian populations of Avena barbata.

We have applied a multivariate log-linear technique to the analysis of interlocus allelic associations among 14 allozyme loci in a sample of 4011 plants from 42 Spanish populations of Avena barbata. The loci fell into three natural groups of five, five, and four loci. The five loci of the first group are invariant, or nearly so, throughout the range of the species. The genetic organization of the loci of this set is defined by a single five-locus genotype; each allele of this predominant genotype is a "wild-type" allele that contributes favorably to adaptedness in all single-locus and multilocus configurations regardless of environment. Although allelic diversity is high in Spain for the nine loci of the second and third sets, log-linear analyses showed that these loci are tied together in Spanish populations through complex networks of overlapping lower-order interlocus interactions. The ancestral Spanish and colonial Californian gene pools are closely similar in allelic composition on a locus-by-locus basis; however, Spanish allelic configurations at two-locus and higher-order levels are usually different from and much less tightly organized than in Californian populations. We conclude that the major force involved in the evolution of the colonial populations was selection that led to reorganization, at the interlocus level, of the ancestral Spanish allelic ingredients into different multilocus genotypes adapted to Californian habitats.

California↗
PubMed1991

[The formation of the microcirculatory bed of the neuromuscular systems of the tongue in human prenatal ontogeny].

A complex of adequate neurohistological and injection methods with use of mathematical analysis of the data obtained has been performed to study prenatal and early postnatal periods of ontogenesis of the microcirculatory bed of the human tongue neuromuscular systems. Certain changes of the degree in organization and structural-functional integration have been revealed; they demonstrate periodicity of the morphological changes of the vasculo-neural complex of the extra- and intrafusal part of the muscular tissue. In the neuromuscular spindles the microvascular network of capillaries is formed, their volumetric part changes in the process of development in greater degree than the microvascular bed of the extrafusal muscular fibers. In formation of the microcirculatory vascular bed of the neuromuscular spindles not only capillaries, getting into them together with nervous fibers, but also microvessels of the surrounding muscle tissue participate. This determines a higher level of the vascularization degree of the intrafusal muscle fibers.

Gestational Age↗
PubMed1988

Nonlinear systems analysis of the hippocampal perforant path-dentate projection. I. Theoretical and interpretational considerations.

1. Nonlinear systems analytic procedures, based on an orthogonalized functional power series approach, were developed for study of the transformational properties of the hippocampal formation. As a testing stimulus, the procedures utilize a train of electrical impulses with randomly varying interimpulse intervals. The specific case was considered of applying such a stimulus to the perforant path, a major afferent to the hippocampal dentate gyrus that arises from the entorhinal cortex. Resulting field potentials evoked within the dentate gyrus are recorded to all impulses in the train. Computational algorithms based on cross-correlations determine the relationship between the interimpulse interval within the random train and amplitude of the evoked dentate potentials. The calculations, which reduce to averaging procedures, were derived for first- and second-order terms, or kernels, of the orthogonalized functional power series. 2. It is proposed that such an approach can be applied to a single component of the complex field potential evoked in the dentate gyrus. This component, the population spike, reflects the action potential discharge of dentate granule cells. Thus, a field potential component for which the underlying neuronal generator is well-known can be analyzed with respect to the transformational characteristics of the network of neurons that influence that generator. Other components of the complex field potential produced by other generators can be ignored. It is shown that this adaptation has the effect of greatly simplifying both the computation and presentation of kernels. 3. As a further consequence of this adaptation, the resulting first- and second-order kernels were shown to have specific interpretations. The first-order kernel represents the average response of the orthodromically driven granule cells to the set of stimuli comprising the random impulse train. The second-order kernel quantitatively characterizes the nonlinearity of the granule cell response, and may be interpreted as a generalized recovery function; i.e., the first input of any pair of stimuli in the train activates the newtork, and the second input tests the modulatory influence of the network excited by the initial input. 4. Most past investigations of nonlinearities of the perforant path-dentate projection have utilized pairs of stimulus impulses. We show here that, for a second-order system, the expected results from paired impulse experiments may be predicted from second-order kernels. Disagreement between the measured and predicted results reflects interactions of a higher order, and thus, greater system complexity.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1992

Predicting responses of nonlinear neurons in monkey striate cortex to complex patterns.

The overwhelming majority of neurons in primate visual cortex are nonlinear. For those cells, the techniques of linear system analysis, used with some success to model retinal ganglion cells and striate simple cells, are of limited applicability. As a start toward understanding the properties of nonlinear visual neurons, we have recorded responses of striate complex cells to hundreds of images, including both simple stimuli (bars and sinusoids) as well as complex stimuli (random textures and 3-D shaded surfaces). The latter set tended to give the strongest response. We created a neural network model for each neuron using an iterative optimization algorithm. The recorded responses to some stimulus patterns (the training set) were used to create the model, while responses to other patterns were reserved for testing the networks. The networks predicted recorded responses to training set patterns with a median correlation of 0.95. They were able to predict responses to test stimuli not in the training set with a correlation of 0.78 overall, and a correlation of 0.65 for complex stimuli considered alone. Thus, they were able to capture much of the input/output transfer function of the neurons, even for complex patterns. Examining connection strengths within each network, different parts of the network appeared to handle information at different spatial scales. To gain further insights, the network models were inverted to construct "optimal" stimuli for each cell, and their receptive fields were mapped with high-resolution spots. The receptive field properties of complex cells could not be reduced to any simpler mathematical formulation than the network models themselves.

Animals↗