Cassaine analogs. VI. Resolution of (plus minus)-7-deoxy-16,17,18,20-tetranorcassaic acid and biological activity of derived esters.
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Alkaloids↗
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From molecular activities and processes to biological function.
This paper describes how biological function can be represented in terms of molecular activities and processes. It presents several key features of a data model that is based on a conceptual description of the network of interactions between molecular entities within the cell and between cells. This model is implemented in the aMAZE database that presently deals with information on metabolic pathways, gene regulation, sub- or supracellular locations, and transport. It is shown that this model constitutes a useful generalisation of data representations currently implemented in metabolic pathway databases, and that it can furthermore include multiple schemes for categorising and classifying molecular entities, activities, processes and localisations. In particular, we highlight the flexibility offered by our system in representing multiple molecular activities and their control, in viewing biological function at different levels of resolution and in updating this view as our knowledge evolves.
Animals↗
The receptor for urokinase-type plasminogen activator and urokinase is translocated from two distinct intracellular compartments to the plasma membrane on stimulation of human neutrophils.
The cellular receptor for urokinase-type plasminogen activator (uPAR) binds pro-urokinase (pro-uPA) and facilitates its conversion to enzymatically active urokinase (uPA). uPA in turn activates surface-bound plasminogen to plasmin, a process of presumed importance for a number of biologic processes including cell migration and resolution of thrombi. We have previously shown that uPAR is expressed on the plasma membrane of circulating neutrophils, and we now report that stimulation with phorbol myristate acetate (PMA), FMLP, or tumor necrosis factor-alpha results in a rapid increase in the expression of uPAR. This process is accompanied by an increased cell-associated plasminogen activation after preincubation of neutrophils with pro-uPA in vitro. By subcellular fractionation of unstimulated neutrophils, 50% of uPAR is recovered in fractions containing latent alkaline phosphatase, corresponding to an intracellular compartment of easily mobilizable secretory vesicles distinct from both primary and specific granules, whereas the remaining 50% of uPAR is associated with a compartment eluting close to the specific granules. In contrast, the ligand pro-uPA is primarily (approximately 80%) found in the specific granules, but small amounts of pro-uPA/uPA (approximately 20%) coelute with latent alkaline phosphatase. Stimulation of neutrophils with FMLP results in translocation of uPAR as well as of pro-uPA from the secretory vesicles, whereas stimulation with PMA is required to translocate material from specific granules. Flow cytometry of neutrophils saturated with exogenous diisopropyl fluorophosphate-uPA shows a large excess (approximately 90%) of unoccupied uPAR on resting as well as FMLP- and PMA-stimulated neutrophils, suggesting a possible role for exogenous pro-uPA in providing neutrophils with a potential for plasminogen activation. These processes may be important for neutrophil extravasation and migration through extracellular matrix and for the contribution of neutrophils to resolution of thrombi.
Biological Transport↗
Crystal structure of schistatin, a disintegrin homodimer from saw-scaled viper (Echis carinatus) at 2.5 A resolution.
This is the first structure of a biological homodimer of disintegrin. Disintegrins are a class of small (4-14 kDa) proteins that bind to transmembrane integrins selectively. The present molecule is the first homodimer that has been isolated from the venom of Echis carinatus. The monomeric chain contains 64 amino acid residues. The three-dimensional structure of schistatin has been determined by the multiple isomorphous replacement method. It has been refined to an R-factor of 0.190 using all the data to 2.5 A resolution. The two subunits of the disintegrin homodimer are related by a 2-fold crystallographic symmetry. Thus, the crystallographic asymmetric unit contains a monomer of disintegrin. The monomer folds into an up-down topology with three sets of antiparallel beta-strands. The structure is well ordered with four intramolecular disulfide bonds. the two monomers are firmly linked to each other through two intermolecular disulfide bridges at their N termini together with several other interactions. This structure has corrected the error in the disulfide bond pattern of the two intermolecular disulfide bridges that was reported earlier using chemical methods. Unique sequence and structural features of the schistatin monomers suggest that they have the ability to bind well with both alphaIIb beta3 and alphav beta3 integrins. The N termini anchored two chains of the dimer diverge away at their C termini exposing the Arg-Gly-Asp motif into opposite directions thus enhancing their binding efficiency to integrins. This is one of the unique features of the present disintegrin homodimer and seems to be responsible for the clustering of integrin molecules. The homodimer binds to integrins apparently with a higher affinity than the monomers and also plays a role in the signaling pathway.
Amino Acid Motifs↗
Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning.
The ability to measure gene expression at single-cell resolution has elevated our understanding of how biological features emerge from complex and interdependent networks at molecular, cellular, and tissue scales. As technologies have evolved that complement scRNAseq measurements with things like single-cell proteomic, epigenomic, and genomic information, it becomes increasingly apparent how much biology exists as a product of multimodal regulation. Biological processes such as transcription, translation, and post-translational or epigenetic modification impose both energetic and specific molecular demands on a cell and are therefore implicitly constrained by the metabolic state of the cell. While metabolomics is crucial for defining a holistic model of any biological process, the chemical heterogeneity of the metabolome makes it particularly difficult to measure, and technologies capable of doing this at single-cell resolution are far behind other multiomics modalities. To address these challenges, we present GEFMAP (Gene Expression-based Flux Mapping and Metabolic Pathway Prediction), a method based on geometric deep learning for predicting flux through reactions in a global metabolic network using transcriptomics data, which we ultimately apply to scRNAseq. GEFMAP leverages the natural graph structure of metabolic networks to learn both a biological objective for each cell and estimate a mass-balanced relative flux rate for each reaction in each cell using novel deep learning models.
Preprint↗
Atypical panic attacks and lack of resolution of mourning.
A number of psychologic and biologic contributors to panic disorder have been identified. Three cases of young adult women who experienced atypical panic attacks are described. The attacks are atypical because they had ideational or situational precipitants and because they were inevitably accompanied by intrusive visual images of a deceased loved one. In each case, there was also the persistence of irrational beliefs and/or unintegrated feelings about the deceased, corroborating that the intrusive images and panic attacks occurred in the context of unresolved mourning. Although the association between panic attacks and intrusive images apparently has not been reported previously, both phenomena have been associated with lack of resolution of mourning. The discussion considers similarities in these cases and in reports of Vietnam veterans suffering from posttraumatic stress disorder and panic attacks. Together, these similarities suggest that unresolved traumas of various kinds may at times contribute to the development of atypical panic attacks accompanied by intrusive visual images.
Adaptation, Psychological↗
X-ray microscopy: preparations for studies of frozen hydrated specimens.
X-ray microscopes provide higher resolution than visible light microscopes. Wet, biological materials with a water thickness of up to about 10 microns can be imaged with good contrast using soft X-rays with wavelengths between the oxygen and carbon absorption edges (at 24 and 43 A). The Stony Brook group has developed and operates a scanning transmission X-ray microscope (STXM) at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory. The microscope is used for imaging with a current resolution of 50 nm, and for elemental and chemical state mapping. Radiation damage imposes a significant limitation upon high resolution X-ray microscopy of room temperature wet specimens. Experience from electron microscopy suggests that cryo techniques allow vitrified specimens to be imaged repeatedly. This is due to the increased radiation stability of biological specimens in the frozen hydrated state. Better radiation stability has been shown recently with a cryo transmission X-ray microscope developed by the University of Göttingen, operating at the BESSY storage ring in Berlin, Germany. At Stony Brook, we are developing a cryo scanning transmission X-ray microscope (CryoSTXM) to carry out imaging and spectro-microscopy experiments on frozen hydrated specimens. This article will give an outlook onto the research projects that we plan to perform using the CryoSTXM.
Animals↗
Near-field scanning optical microscopy in cell biology and cytogenetics.
Light microscopy has proven to be one of the most versatile analytical tools in cell biology and cytogenetics. The growing spectrum of scientific knowledge demands a continuous improvement of the optical resolution of the instruments. In far-field light microscopy, the attainable resolution is dictated by the limit of diffraction, which, in practice, is about 250 nm for high-numerical-aperture objective lenses. Near-field scanning optical microscopy (NSOM) was the first technique that has overcome this limit up to about one order of magnitude. Typically, the resolution range below 100 nm is accessed for biological applications. Using appropriately designed scanning probes allows for obtaining an extremely small near-field light excitation volume (some tens of nanometers in diameter). Because of the reduction of background illumination, high contrast imaging becomes feasible for light transmission and fluorescence microscopy. The height of the scanning probe is controlled by atomic force interactions between the specimen surface and the probe tip. The control signal can be used for the production of a topographic (nonoptical) image that can be acquired simultaneously. In this chapter, the principle of NSOM is described with respect to biological applications. A brief overview of some requirements in biology and applications described in the literature are given. Practical advice is focused on instruments with aperture-type illumination probes. Preparation protocols focussing on NSOM of cell surfaces and chromosomes are presented.
Animals↗
Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy.
BACKGROUND: Ribosomes are complex macromolecular machines that perform the translation of the genetic message. Cryo-electron microscopic (cryo-EM) maps of the Escherichia coli 70S ribosome are approaching a resolution of 10 A and X-ray maps of the 30S and 50S subunits are now available at 5 A. These maps show a lot of details about the inner architecture of the ribosome and ribosomal RNA helices are clearly visible. However, in the absence of further biological information, even at the higher resolution of the X-ray maps many rRNA helices can be placed only tentatively. Here we show that genetic tagging in combination with cryo-EM can place and orient double-stranded RNA helices with high accuracy. RESULTS: A tRNA sequence inserted into the E. coli 23S ribosomal RNA gene, at one of the points of sequence expansion in eukaryotic ribosomes, is visible in the cryo-EM map as a peripheral 'foot' structure. By tracing its acceptor-stem end, the location of helix 63 in domain IV and helix 98 in domain VI of the 50S subunit could be precisely determined. CONCLUSIONS: Our study demonstrates for the first time that features of a three-dimensional cryo-EM map of an asymmetric macromolecular complex can be interpreted in terms of secondary and primary structure. Using the identified helices as a starting point, it is possible to model and interpret, in molecular terms, a larger portion of the ribosome. Our results might be also useful in interpreting and refining the current X-ray maps.
Base Sequence↗
High-resolution confocal imaging and three-dimensional rendering.
Intrinsic opacity and inhomeogeniety of most biological tissues have prevented the efficient light penetration and signal detection for high-resolution confocal imaging of thick tissues. Here, we summarize recent technical advances in high-resolution confocal imaging for visualization of cellular structures and gene expression within intact whole-mount thick tissues. First, we introduce features of the FocusClear technology that render biological tissue transparent and thus improve the light penetration and signal detection. Next, a universal fluorescence staining method that labels all nuclei and membranes is described. We then demonstrate the postrecording image processing techniques for 3D visualization. From these images, regions of interest in the whole-mount brain can be segmented and volume rendered. Together, these technical advances in confocal microscopy allow visualization of structures within whole-mount tissues up to 1mm thick at a resolution similar to that of the observation of single cells in culture. Practical uses and limitations of these techniques are discussed.
Animals↗
A Raman and infrared spectroscopic investigation of biological hydroxyapatite.
Raman spectra were acquired on ox femur samples treated with hydrazine to remove the organic components of bone. A large increase in the signal-noise ratio of the mineral spectrum resulted from the exposure of the mineral surface and the removal of fluorescent components of the organic matrix. The effect of hydrazine treatment of the mineral matrix has been reinvestigated and shown to be slight on the basis of second derivative FTIR data. This is the first time that this high resolution technique has been applied to biological minerals.
Animals↗
Watching the components of photosynthetic bacterial membranes and their in situ organisation by atomic force microscopy.
The atomic force microscope has developed into a powerful tool in structural biology allowing information to be acquired at submolecular resolution on the protruding structures of membrane proteins. It is now a complementary technique to X-ray crystallography and electron microscopy for structure determination of individual membrane proteins after extraction, purification and reconstitution into lipid bilayers. Moving on from the structures of individual components of biological membranes, atomic force microscopy has recently been demonstrated to be a unique tool to identify in situ the individual components of multi-protein assemblies and to study the supramolecular architecture of these components allowing the efficient performance of a complex biological function. Here, recent atomic force microscopy studies of native membranes of different photosynthetic bacteria with different polypeptide contents are reviewed. Technology, advantages, feasibilities, restrictions and limits of atomic force microscopy for the acquisition of highly resolved images of up to 10 A lateral resolution under native conditions are discussed. From a biological point of view, the new insights contributed by the images are analysed and discussed in the context of the strongly debated organisation of the interconnected network of membrane-associated chlorophyll-protein complexes composing the photosynthetic apparatus in different species of purple bacteria.
Bacteria↗
[On work of the Bureau of the Department of Medical-Biological Sciences for 1960-1961 and problems of scientific-research institutions of the Department in the light of resolutions of the 22d Congress of the Communist Party of the Soviet Union].
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Biological Science Disciplines↗
Enantiospecific analysis by capillary electrophoresis: applications in drug metabolism and pharmacokinetics.
Enantiospecific analysis has an important role in drug metabolism and pharmacokinetic investigations and its now no longer acceptable to determine total drug, or metabolite, concentrations following the administration of a racemate. Inspite of the fact that capillary electrophoresis (CE) has become an essential technique in pharmaceutical and enantiospecific analysis, the chromatographic methodologies remain the most commonly used approach for the determination of the enantiomeric composition of drugs in biological fluids. The application of CE to bioanalysis has been slow, which is in part associated with the complexity of biological matrices together with the relatively poor concentration limits of detection achievable. However, as a result of its versatility, high separation efficiency, minimal sample requirements, speed of analysis and low consumable expense CE is likely to play an increasingly significant role in the area. This review present an overview of enantiospecific CE in bioanalysis in which the approaches to enantiomeric resolution and the problems associated with biological matrices are briefly discussed. The application of enantiospecific CE to samples of biological origin is illustrated using examples where the methodology has either solved an analytical problem, or provided a useful alternative to the currently available chromatographic methods. Such improvements in methodology are associated with either the high separation efficiency and/or microanalytical capabilities of the technique. Enantiospecific CE will not replace the chromatographic methodologies but does provide the bioanalyst with a useful addition to his armamentarium.
Electrophoresis, Capillary↗
Molecular karyotyping in sarcoma diagnostics and research.
Conventional cytogenetic and molecular genetic studies have both clinical and biological significance in sarcomas. However, the resolution of these methods does not always suffice to screening of novel, specific genetic changes, such as small deletions, amplifications, and fusion genes. Tumor-specific chromosomal translocations revealed by cytogenetic and molecular methods play a decisive role in the differential diagnosis of sarcomas. The novel molecular karyotyping techniques have proven to be powerful in the screening of clinically and biologically relevant molecular changes in human neoplasias. A variety of platforms for molecular karyotyping is available, e.g., arrayed cDNA clones or oligonucleotides that can be used in microarray-based comparative genomic hybridization (CGH) and gene expression analysis. We review here the clinically most relevant cytogenetic and molecular changes in sarcomas and describe latest microarray techniques for screening of clinically relevant gene copy number and expression changes.
Genetic Testing↗
Use of laser microdissection in complex tissue.
Concomitant with the rapid development in biomedical knowledge, including the methods of molecular biology and proteomics, and the manufacture of ever more precise optical instruments, powerful lasers, and sophisticated microcomputing hardware and software, laser microdissection systems have emerged which are now entering the field of routine research. Today, several devices are commercially available, congresses devoted to the latest advances in laser microdissection are now held on regular occasions, and the number of publications based on the use of these techniques has risen to over 250. With laser microdissection, histological treatment, such as chemical or immunological fixation and staining, can readily be combined with methods suitable for molecular biology or proteomics. As the optical, technical, and methodological resolution of polymerase chain reaction (PCR) and microdissection increases, genetic and phenotypic studies of biological material are possible even at the level of single cells and subcellular elements. Moreover, questions such as the paracrine interaction of cells within complex tissues, the development of cancer, and the role of single cells in tissue remodeling or development on the microscopic and molecular level can now be addressed precisely at the molecular level. This chapter reviewed the development of laser microdissection platforms, its potential impact on the future of research, and how, in particular, these technologies can be successfully integrated into modern research and routine histopathological studies of complex tissue.
Animals↗
Aspects of cryofixation and cryosectioning for the observation of bulk biological samples in the hydrated state by cryoelectron microscopy.
Cryoelectron microscopy allows the observation of hydrated samples at high spatial resolution, and it would be of great interest in biology to apply this method to cells and tissues. However, because of technical problems, the cryo-observation of frozen hydrated ultrathin sections of bulk material has not become an established method. The major limitations are due to the difficulty of achieving the vitrification of such material, and the structural deformation caused by ultrathin sectioning: 1. The vitrification of cells in a physiological environment requires high-pressure freezing. However, new results suggest that the pressure may alter the ultrastructure of the sample. 2. Cryosectioning compresses structures in the cutting direction about 40%. This deformation does not necessarily destroy the character of macromolecular assemblies, but since it depends on the properties of the material, internal standards cannot be used to correct for the deformation of all the structures in a cell.
Animals↗
Single-cell elastography: probing for disease with the atomic force microscope.
The atomic force microscope (AFM) is emerging as a powerful tool in cell biology. Originally developed for high-resolution imaging purposes, the AFM also has unique capabilities as a nano-indenter to probe the dynamic viscoelastic material properties of living cells in culture. In particular, AFM elastography combines imaging and indentation modalities to map the spatial distribution of cell mechanical properties, which in turn reflect the structure and function of the underlying cytoskeleton. Such measurements have contributed to our understanding of cell mechanics and cell biology and appear to be sensitive to the presence of disease in individual cells. This chapter provides a background on the principles and practice of AFM elastography and reviews the literature comparing cell mechanics in normal and diseased states, making a case for the use of such measurements as disease markers. Emphasis is placed on the need for more comprehensive and detailed quantification of cell biomechanical properties beyond the current standard methods of analysis. A number of technical and practical hurdles have yet to be overcome before the method can be of clinical use. However, the future holds great promise for AFM elastography of living cells to provide novel biomechanical markers that will enhance the detection, diagnosis, and treatment of disease.
Biophysics↗