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Ultrastructural analysis during germination and outgrowth of Bacillus subtilis spores.

Electron microscopy of thin sections of dormant and germinating spores of Bacillus subtilis 168 revealed a progressive change in the structure of the cortex, outer spore coat, and inner spore coat. The initial changes were observed in the cortex region, which showed a loose fibrous network within 10 min of germination, and in the outer spore coat, which began to be sloughed off. The permeability of the complex outer spore layers was modified within 10 min, since, at this time, the internal structures of the spore coat were readily stainable. A nicking degradation action of the laminated inner spore coat began at 20 min, and this progressed for the next 20 min leading to the loosening of the inner spore coat. By 30 min, the outer spore coat showed signs of disintegration, and at 40 min, both the outer and inner spore coats were degraded extensively. At 30 to 40 min, a period just preceding net deoxyribonucleic acid synthesis, mesosomes became very prominent in the inner spore core and the cell wall began to thicken around the spore core. At 50 min, an emerging cell was observed, and by 60 min, there was clear evidence for elongation of the emerging cell and the presence of two nuclear bodies. At 90 min, elongation had been followed by the first cell division. There was evidence for spore coat fragments at the opposite poles of the dividing cell.

Bacillus subtilis

Quantitative analysis of electroencephalograms: is there chaos in the future?

The history of quantitative, computerized electroencephalogram (EEG) analysis is reviewed. It is shown that, until very recently, the basic approach to EEG analysis involved the assumption that the EEG is stochastic. Consequently, statistical pattern recognition techniques, segmentation procedures, syntactic methods, knowledge-based approaches, and even artificial neural network methods have been developed with different levels of success. A fundamentally different approach to computerized EEG analysis, however, is making its way into the laboratories. The basic idea, inspired by recent advances in the area of non-linear dynamics, and especially the theory of chaos, is to view an EEG as the output of a deterministic system of relatively simple complexity, but containing non-linearities. This suggests that studying the geometrical dynamics of EEGs, and the development of neurophysiologically realistic models of EEG generation may produce more successful automated EEG analysis techniques than the classical, stochastic methods. Evidence supporting the non-linear dynamics paradigm is reviewed, and possible research paths are indicated.

Algorithms

Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution.

The structure of the tri-N-acetylchitotriose inhibitor complex of hen egg-white lysozyme has been refined at 1.75 A resolution, using data collected from a complex crystal with ligand bound at less than full occupancy. To determine the exact value of the inhibitor occupancy, a model comprising unliganded and sugar-bound protein molecules was generated and refined against the 1.75 A data, using a modified version of the Hendrickson & Konnert least-squares procedure. The crystallographic R-factor for the model was found to fall to a minimum at 55% bound sugar. Conventional refinement assuming unit occupancy was found to yield incorrect thermal and positional parameters. Application of the same refinement procedures to an earlier 2.0 A data set, collected independently on different complex crystals by Blake et al. gave less consistent results than the 1.75 A refinement. From an analysis of the high resolution structure a detailed picture of the protein-carbohydrate interactions in the non-productive complex has emerged, together with the conformation and mobility changes that accompany ligand binding. The specificity of interaction between the protein and inhibitor, bound in subsites A to C of the active site, is seen to be generated primarily by an extensive network of hydrogen bonds, both to the protein itself and to bound solvent molecules. The latter also play an important role in maintaining the structural integrity of the active site cleft in the apo-protein.

Binding Sites

Axon-Schwann cell networks are regular components of nodal regions in normal large nerve fibres of cat spinal roots.

The paranodal occurrence of axon-Schwann cell networks (ASNs), which are entities assumed to take part in the removal of degenerate axonal material, was examined quantitatively by electron microscopical serial section analysis in normal cat ventral and dorsal spinal roots. In nerve fibres greater than or equal to 10 microns in diameter 88% of the nodal regions in the ventral roots and 97% in the dorsal roots showed ASN complexes, which especially in the ventral roots often consisted of many segregated axoplasmic portions. The corresponding frequencies in fibres less than 10 microns were 28% and 62% in the ventral and the dorsal roots, respectively. ASN complexes were rare in fibres less than 5 microns. The results show that the ASN is a part of the normal paranodal architecture in large myelinated nerve fibres. The ASN occurrence seems to differ with neurone type.

Animals

Dissecting spatial patterning and signaling with directional diffusion in spatial multi-omics.

Spatial multi-omics sequencing enables the simultaneous profiling of transcriptomics, proteomics, and epigenomics at a spatial resolution, offering insights into complex tissue organization and molecular regulation. However, the effective integration of multiple omics modalities in a spatial context remains a major challenge. Here, we present SpaDDM, a spatial multi-omics integration framework based on directional diffusion models (DDMs), which supports spatial pattern identification, cross-omics alignment, and inter-and intracellular signaling flow analysis. SpaDDM employs DDM-based graph networks to learn omics-specific representations by jointly incorporating spatial coordinates and molecular measurements within each modality, followed by an attention mechanism to align features across modalities. We benchmarked SpaDDM on diverse spatial multi-omics datasets, including transcriptomics-epigenomics and transcriptomics-proteomics combinations across multiple tissues and species. SpaDDM consistently outperformed existing methods by more accurately deciphering spatial tissue patterns and effectively reducing the boundary noise between spatial regions. Moreover, the learned low-dimensional coembedded representations of individual cells serve as integral mediators for inferring the signaling flows that underlie spatial patterning. Finally, we demonstrated that SpaDDM alignment of complementary information across multi-omics layers facilitates cross-omics translation and significantly improves the prediction of cell state alignments.

Multiomics

Quantitative analysis of ventral denticular patterns of Drosophila melanogaster larvae and the regulation of the bithorax complex.

A quantitative model of the effect of the bithorax complex on segmentation is presented which could explain the known data of the spatiotemporal regulation of key gene complex during early Drosophila development, in relation to their effects on some of the segmentation landmarks. The model tries to put together the two different genetic levels, the genotypic and the phenotypic. At the genotypic level, a minimal cross-regulatory network of the different genes involved, Antp, Ubx, abd-A and Abd-B which explains the reported levels of expressions of these genes. At the phenotypic level, the pattern of the ventral denticle belts across the larva which are characteristics of the different segments have been compared by calculating a value of the degree of similarity in the case of the wild-type and several mutant combinations. Finally the two parts of the model are combined, showing that a satisfactory agreement between the two can be achieved. Therefore, this work is a first attempt to develop a method which will provide an explanatory solution of the old question in morphogenesis of how the phenotype is directed by the genotype of a cell or organism.

Animals

Evidence for an involvement of actin in the positioning and motility of centrosomes.

Cultured human polymorphonuclear leukocytes exposed to the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) spread on the substratum and undergo centrosome splitting. The two centrioles may separate by a distance of several micrometers, each being surrounded by an aster of microtubules. Here we show that the centriole/aster complexes are in constant, rapid motion through the cytoplasm, carrying with them some of the cytoplasmic granules while pushing aside others, or deforming and displacing the nucleus. An analysis of this unique motility phenomenon was undertaken. We show that intact microtubules are required for TPA-induced centrosome splitting and aster motility, but not for cell spreading. More importantly, disruption of the actin network inhibits both centrosome splitting and cell spreading, and even reverses splitting (induces convergence and fusion of asters) in polymorphonuclear leukocytes pretreated with TPA alone. These observations indicate the existence of a dynamic relationship between microtubules and actin networks and provide evidence for a role of actin in determining the position of the centrosome by way of interaction with the microtubules radiating from it.

Actins

MPAC: a computational framework for inferring pathway activities from multi-omic data.

Fully capturing cellular state requires examining genomic, epigenomic, transcriptomic, proteomic, and other assays for a biological sample and comprehensive computational modeling to reason with the complex and sometimes conflicting measurements. Modeling these so-called multi-omic data is especially beneficial in disease analysis, where observations across omic data types may reveal unexpected patient groupings and inform clinical outcomes and treatments. We present Multi-omic Pathway Analysis of Cells (MPAC), a computational framework that interprets multi-omic data through prior knowledge from biological pathways. MPAC leverages network relationships encoded in pathways through a factor graph to infer consensus activity levels for proteins and associated pathway entities from multi-omic data, runs permutation testing to eliminate spurious activity predictions, and groups biological samples by pathway activities to allow identifying and prioritizing proteins with potential clinical relevance, e.g., associated with patient prognosis. Using DNA copy number alteration and RNA-seq data from head and neck squamous cell carcinoma patients from The Cancer Genome Atlas as an example, we demonstrate that MPAC predicts a patient subgroup related to immune responses not identified by analysis with either input omic data type alone. Key proteins identified via this subgroup have pathway activities related to clinical outcome as well as immune cell compositions. Our MPAC R package, available at https://bioconductor.org/packages/MPAC, enables similar multi-omic analyses on new datasets.

Journal Article

Computational sequence analysis revisited: new databases, software tools, and the research opportunities they engender.

The increasing quantity and complexity of sequences and structural data for proteins and nucleic acids create both problems and opportunities for biomedical researchers. Fortunately, a new generation of practical computer tools for data analysis and integrated information retrieval is emerging. Recent developments in fast database searching, multiple sequence alignment, and molecular modeling are discussed and windows-based, mouse-driven software for CD-ROM and network information retrieval are described. Each method is illustrated with a practical example pertinent to lipid research. In particular, the connection among cholesteryl ester transfer protein, bactericidal permeability-increasing protein, and lipopolysaccharide-binding proteins is determined; novel repetitive sequence motifs in mammalian farnesyltransferase subunits and related yeast prenyltransferases are derived; biochemical insights from a three-dimensional model of human apolipoprotein D based on two insect lipocalins are discussed; the relationship between apolipoprotein D and gross cystic disease fluid protein from human breast is reviewed; and prospects for modeling apolipoprotein E-related proteins are described. In addition, information on a number of general and special-purpose sequence, motif, and structural databases is included.

Amino Acid Sequence

MPAC: a computational framework for inferring pathway activities from multi-omic data.

MOTIVATION: Fully capturing cellular state requires examining genomic, epigenomic, transcriptomic, proteomic, and other assays for a biological sample and comprehensive computational modeling to reason with the complex and sometimes conflicting measurements. Modeling these so-called multi-omic data is especially beneficial in disease analysis, where observations across omic data types may reveal unexpected patient groupings and inform clinical outcomes and treatments. RESULTS: We present Multi-omic Pathway Analysis of Cells (MPAC), a computational framework that interprets multi-omic data through prior knowledge from biological pathways. MPAC leverages network relationships encoded in pathways through a factor graph to infer consensus activity levels for proteins and associated pathway entities from multi-omic data, runs permutation testing to eliminate spurious activity predictions, and groups biological samples by pathway activities to allow identifying and prioritizing proteins with potential clinical relevance, e.g. associated with patient prognosis. Using DNA copy number alteration and RNA-seq data from head and neck squamous cell carcinoma patients from The Cancer Genome Atlas as an example, we demonstrate that MPAC predicts a patient subgroup related to immune responses not identified by analysis with either input omic data type alone. Key proteins identified via this subgroup have pathway activities related to clinical outcome as well as immune cell composition. Our MPAC R package enables similar multi-omic analyses on new datasets. AVAILABILITY AND IMPLEMENTATION: The MPAC package is available at Bioconductor https://bioconductor.org/packages/MPAC.

Humans

Morphological analysis of neovascularization at early stages of rat splenic autografts in comparison with tumor angiogenesis.

This study was undertaken to reveal the neovascularization at early stages of splenic autografts three-dimensionally, to illustrate the differences between it and tumor angiogenesis, and to establish its origin. Early vascular formation after transplantation of the rat spleen or Walker tumor into the major omentum was examined by using a video macroscope, vascular casting methods and the organ culture technique. A complex vascular network layer (vascular cortex) was first formed beneath the capsule of an autograft; later, vascular buds grew from this network toward the necrotic center. They anastomosed and changed into a form resembling withered twigs (vascular medulla). Tumor angiogenesis did not present such morphological features and was characterized by capillary loop formation with a columnar vertex resembling an "inverted V". This fundamental structure did not change throughout angiogenesis except for dilation and irregularity of vascular diameter. The organ culture technique demonstrated that the preliminary vasculature was formed in splenic autografts by regeneration of preexisting vessels in the graft and not by invading capillaries. Transmission electron microscopy showed that the cells present had characteristics of sinus endothelial cells. These results suggest that preexisting sinus endothelial cells rearrange themselves after devascularization and reconstruct a new vasculature that anastomoses with the penetrating capillaries. This mechanism establishes vascular circulation at an early stage, and accelerates regeneration of the splenic autograft before complete necrosis.

Animals

Antibody-induced conformational changes result in enhanced avidity of antibodies to different antigenic sites on the tick-borne encephalitis virus glycoprotein.

By the use of monoclonal antibodies we have recently defined eight distinct epitopes on the structural glycoprotein of tick-borne encephalitis (TBE) virus which differ with respect to location, function, or serological specificity (Heinz et al, Virology 126, 525-537, 1983). The present investigation reveals a complex network of interactions between antibodies directed against distinct nonoverlapping epitopes leading to enhanced binding of certain antibodies in the presence of bound second antibodies. The enhancement between antibody pairs can be either unidirectional or bidirectional. In addition, there are domains of predilection, which bind enhanceable antibodies (domain A) whereas others bind antibodies which preferentially induce enhancement (domain B). These domains represent structurally unrelated entities, domain A being sensitive to denaturation and fragmentation and domain B being resistant. Quantitative evaluation of binding data by Scatchard analysis revealed that the observed enhancement phenomenon is due to a two- to sixfold increase of antibody avidity. In the system described, enhancement of antibody binding is not dependent on antibody bivalency since it could also be demonstrated with purified Fab fragments acting either as enhanced or as enhancing antibody. It is therefore concluded that binding of antibodies to certain epitopes on the TBE virus glycoprotein induces conformational changes in distant parts of the molecule which can result in increased avidity of antibodies directed to conformationally changed epitopes. A possible explanation for the origin of this enhancement phenomenon is presented.

Antibodies, Monoclonal

Deciphering differential mRNA and lncRNA expression profiles in response to PEG simulated drought stress in cucumber (Cucumis sativus L.).

Cucumber (Cucumis sativus L.), a vital fruit vegetable of the Cucurbitaceae family, originated in India ∼ 3000 years ago. It is widely used in the culinary, therapeutic, and cosmetic sectors. Cucumber cultivation is significantly impacted by drought stress, especially in arid and semi-arid regions. This study investigates the molecular response to drought using two contrasting cucumber lines: WBC-23-2 (drought-tolerant) and DGPC-59 (drought-sensitive). Drought was simulated using polyethylene glycol (PEG), and effects on physiological and biochemical traits were evaluated. The tolerant line exhibited reduced leaf wilting and higher relative water content (RWC). Based on these physiological markers, transcriptomic profiling was employed to identify the underlying regulatory networks. Analysis identified 4,736 DEGs, suggesting that the tolerant line's superior resilience is driven by preferential activation of genes involved in photosynthesis and glutathione metabolism. Conversely, the sensitive genotype showed enrichment in organonitrogen compound catabolism and water deprivation response. This divergence is further reflected in the regulation of 155 transcription factors (TFs) across various families, indicating distinct regulatory architectures between the two lines. Additionally, 774 drought-responsive long non-coding RNAs (lncRNAs) were identified, acting via cis, trans, and competing endogenous RNA (ceRNA) mechanisms to modulate gene expression. Key candidate genes associated with drought tolerance included WAT1-related protein At5g64700, thaumatin-like protein, berberine bridge enzyme-like 18, probable WRKY transcription factor, and pathogenesis-related protein 1. This study reveals a complex regulatory network of mRNAs, lncRNAs, and TFs underlying drought response and provides a valuable foundation for breeding drought-resilient cucumber cultivars. A web-based genomic resource, CsDTDb, has been developed and made publicly available to facilitate future functional genomics studies related to drought tolerance in cucumber.

DEGs

The t complex polypeptide 1 (TCP-1) is associated with the cytoplasmic aspect of Golgi membranes.

The t complex polypeptide 1 (TCP-1) is a protein of unknown function expressed in large amounts during spermatogenesis. Rat monoclonal antibodies recognizing TCP-1 have been prepared and used to immunoprecipitate and Western blot a 57 kd protein from germ cell and tissue culture cell extracts. In tissue culture cells, indirect immunofluorescent localization of antigen indicated a perinuclear distribution similar to that of the Golgi apparatus. Analysis of the TCP-1 distribution in tissue culture cells showed that the polypeptide was associated with the cytoplasmic aspect of membranes of the trans-Golgi network (TGN). The distribution in spermatids suggested that TCP-1 was localized to structures often associated with the developing acrosome. The TCP-1 antigenic epitopes are highly conserved, allowing the protein to be identified in cells across a wide variety of vertebrate species and tissues. These experiments suggest that TCP-1 may be essential for transport of proteins through the exocytic pathway in all cells and required in large amounts for acrosome formation in developing spermatids.

Acrosome

Fusimotor reflex profiles of individual triceps surae primary muscle spindle afferents assessed with multi-afferent recording technique.

The experiments were performed on 21 cats anaesthetized with alpha-chloralose. The aim of the study was to investigate sets of simultaneously recorded spindle afferents (2-4 in each set) from the triceps surae muscle (GS) with respect to the pattern of fusimotor reflex effects evoked by different types of ipsi- and contralateral reflex stimulation. The afferents' responses to sinusoidal stretching of the GS muscle were determined and the fusimotor reflex effects were assessed by comparing the afferent responses (i.e. the mean rate of firing and the depth of modulation) elicited during reflex stimulation with those evoked in absence of any reflex stimulus. Natural of electrical activations of ipsi- and contralateral muscle, skin and joint receptor afferents were used as reflex stimuli. The spindle afferents were influenced by several modalities and from wide areas, with a majority responding to both ipsi- and contralateral stimuli. A particular reflex stimulus often caused different effects on different afferents, and the various reflex stimuli seldom gave similar effects on a particular afferent. Multivariate analysis revealed that the variation in response profiles among simultaneously recorded afferents were as great as between afferents recorded on different occasions. This suggests that the individualized response prifiles, observed in earlier investigations, represent a very diversified reflex control of the spindle primary afferents, and are not a reflection of changes in the setting of the spinal interneuronal network, occurring during the time interval between the recordings of different units. Also, there was no relation between the conduction velocity of the afferents and the reflex profiles of the afferents, but non-linear relations were found between effects elicited by different types of stimuli. Indications were also found that it may be possible to separate the population of GS muscle spindles into subgroups, according to the fusimotor effects exhibited by activation of various categories of ipsi- and contralateral receptor afferents. It is concluded that one possible way of making the very complex reflex system controlling the muscle spindles intelligible may be a combination of multiple simultaneous recordings of spindle afferents and multivariate analysis.

Afferent Pathways

Role of IFIT1 and IFIT3 in systemic lupus erythematosus: modeling a diagnosis and exploring immune regulation.

Systemic lupus erythematosus (SLE) is a complex autoimmune disorder characterized by multi-organ involvement and a protracted clinical course. Current diagnostic strategies, which rely heavily on clinical symptoms and serology, are often insufficient for early detection. Therefore, highly accurate diagnostic biomarkers are urgently needed to facilitate early intervention and optimize personalized treatment strategies. D atasets GSE61635 and GSE135779 were integrated to identify differentially expressed genes. Weighted gene co-expression network analysis (WGCNA) was performed to isolate the module with the strongest clinical relevance. Mendelian randomization and single‑cell RNA‑seq were used to identify key disease‑relevant genes. A diagnostic model was then constructed, and gene set variation analysis (GSVA), along with gene set enrichment analysis (GSEA), was conducted to elucidate the underlying molecular pathways. IFIT1 and IFIT3 were identified as 2 core genes highly expressed in monocytes and T cells of SLE patients. Functional enrichment analysis revealed that these genes were enriched in immune-related pathways, metabolic pathways related to inflammation and genomic stability. The diagnostic model showed good accuracy, with an area under the curve (AUC) of 0.974 on the training set and 0.912 on the validation set. IFIT1 and IFIT3 represent promising biomarkers for diagnosing SLE and appear to mediate key immune and metabolic disturbances. Furthermore, the developed model serves as an accurate and reliable instrument for early diagnosis and personalized therapy. Large-scale clinical studies are warranted to further validate these findings and evaluate their clinical application.

Humans

Optimizing eco-engineering pedogenesis of bauxite residues: Synergistic effects of humus and FeSO4/sulfur on microbial community and function.

Eco-engineered pedogenesis represents a promising approach for soil amelioration of bauxite residues (BRs) through exogenous organic matter. However, the role of humus in mediating this process remains poorly understood, significantly impeding the eco-engineering rehabilitation of BRs. In this study, we conducted pot experiments and subsequent microbial analysis to evaluate the individual improvement of humic acid (HA), fulvic acid (FA), and corn straw (SWZ) on the BRs' pedogenesis. High-throughput sequencing analysis revealed that both FA and SWZ were more effective than HA in steering microbial community assembly, as community diversity, dominant taxa enrichment, and species' interaction were all significantly higher (p < 0.05) in the FA/SWZ treatments than in HA treatments. Notably, the combination of FA with FeSO4 specifically enriched halophilic taxa, while FA coupled with sulfur (S) significantly improved the connectivity and complexity of the microbial network, as the average connection degree increasing from 1.008 to 1.113. Hydrolytic enzyme activity assays further indicated that FA, especially when combined with S, was the most effective treatment in restoring microbial function during BR pedogenesis. These findings highlight FA as a critical driver of microbial restructuring and functional recovery in BRs. Moreover, its efficacy can be enhanced by co-amendment with FeSO4 or S. This study provides important theoretical and practical insights for optimizing organic-inorganic amendment strategies to accelerate the eco-engineering pedogenesis of bauxite residues.

Humic Substances

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