Intracellular protein trafficking into catecholamine storage vesicles: novel chimeric photoproteins visualized by deconvolution fluorescence microscopy.
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Animals↗
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Results for “cell deconvolution”
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The beta cell glucose stimulus-response curve in normal humans assessed by insulin and C-peptide secretion rates.
Insulin and C-peptide secretion rates have been measured and compared in 12 nondiabetic subjects to characterize the glucose stimulus-response of B cell secretion in man. On three different days, glucose concentrations were clamped for 150 minutes at 7.5, 10, and 15 mmol/L, respectively. Plasma samples taken during the clamps were assayed for C-peptide and insulin. C-peptide secretion rates were estimated by the technique of deconvolution. Model-based estimation of insulin secretion rates from insulin concentrations yielded concordant results. In response to glucose, C-peptide concentrations rose less quickly than did insulin concentrations, but the estimated first- and second-phase secretion rates were similar when assessed from either the C-peptide or insulin concentrations. First-phase secretion peaks were larger than inspection of the plasma concentration data might suggest, with median values of 1.3, 2.0, and 2.9 nmol/min for C-peptide in response to 7.5, 10, and 15 mmol/L glucose clamp levels, respectively. The second-phase reached steady state by 90 to 120 minutes, with median C-peptide secretion rates of 0.31, 0.56, and 0.85 nmol/min after 120 minutes at 7.5, 10, and 15 mmol/L, respectively. The slopes of the curves of steady-state insulin and C-peptide secretion rates v the four glucose levels (basal plus the three clamp levels) were maximally steep between 7.5 and 10 mmol/L in the majority of subjects, consistent with in vitro sigmoidal responses. A characterization of the secretory response of the B cell of normal humans at different glucose concentrations has been obtained. With appropriate models, insulin secretion rates may be estimated from either plasma insulin or C-peptide concentration data.
Adult↗
Blind deconvolution of 3D transmitted light brightfield micrographs.
The blind deconvolution algorithm for 3D transmitted light brightfield (TLB) microscopy, published previously [Holmes et al. Handbook of Biological Confocal Microscopy (1995)], is summarized with example images. The main emphasis of this paper is to discuss more thoroughly the importance and usefulness of this method and to provide more detailed evidence, some being quantitative, of its necessity. Samples of horseradish peroxidase (HRP)-stained pyramidal neurones were prepared and evaluated for the ability to see fine structures clearly, including the dendrites and spines. It is demonstrated that the appearance of fine spine structure, and means of identifying spine categories, is made possible by using blind deconvolution. A comparison of images of the same sample from reflected light confocal microscopy, which is the conventional light microscopic way of viewing the 3D structure of these HRP-stained samples, shows that the blind deconvolution method is far superior for clearly showing the structure with less distortion and better resolution of the spines. The main significance of this research is that it is now possible to obtain clear images of 3D structure by light microscopy of absorbing stains. This is important because the TLB microscope is probably the most widely used modality in the life-science laboratory, yet, until now, there has been no reliable means for it to provide visualization of 3D structure clearly. The main importance of the blind deconvolution approach is that it obviates the need to measure the point spread function of the optical system, so that it now becomes realistic to provide a 3D light microscopic deconvolution method that can be pervasively used by microscopists.
Algorithms↗
Intracellular expression of Vitreoscilla hemoglobin modifies microaerobic Escherichia coli metabolism through elevated concentration and specific activity of cytochrome o.
The function of the reversible oxygen-binding hemoprotein from Vitreoscilla (VHb), which enhances oxygen-limited cell growth and recombinant protein production when functionally expressed in Escherichia coli, was investigated in wild-type E. coli and in E. coli mutants lacking one of the two terminal oxidases, cytochrome o complex (aerobic terminal oxidase, Cyo) or cytochrome d complex (microaerobic terminal oxidase, Cyd). Deconvolution of VHb, cytochrome o, and cytochrome d bands from in vivo absorption spectra revealed a 5-fold enhancement in cytochrome o content and a 1.5-fold increment in cytochrome d by VHb under microaerobic environments (dissolved oxygen less than 2% air saturation). Based upon oxygen uptake kinetics measurements of these mutants, the apparent oxygen affinity of the Cyo(+), Cyd(-) E. coli was increased in the presence of VHb, but no difference in the apparent K(m) was observed for the Cyo(-), Cyd(+) strain. Results suggest that the expression of VHb in E. coli increases the level and activity of terminal oxidases and thereby improves the efficiency of microaerobic respiration and growth.
Aerobiosis↗
Pathophysiology of hyperinsulinemia following pancreas transplantation: altered pulsatile versus Basal insulin secretion and the role of specific transplant anatomy in dogs.
OBJECTIVE: To evaluate the effect of the anatomical alterations of the pancreas required for transplantation on pulsatile insulin secretion. SUMMARY BACKGROUND DATA: Pancreas transplantation involves anatomical changes that have unknown consequences on glucose homeostasis. Pancreas transplant patients are free of exogenous insulin requirements, yet appear to have endogenous hyperinsulinemia. The effect of surgical alterations on posttransplant insulin release is not completely known, specifically with regards to possible alterations in patterns of pulsatile release. METHODS: Pulsatile and invariant basal insulin secretion was studied in normal dogs (n = 4) and three canine models of the anatomical alterations of pancreas transplantation: 70% partial pancreatectomy (PPX, n = 4), partial pancreatectomy with splenocaval venous diversion (SC, n = 4), and partial pancreatectomy with remnant autotransplantation (PAT, n = 4). Plasma insulin kinetics were determined for each dog, and then blood sampled at 1-minute intervals in a fasted and IV glucose-stimulated state twice to delineate the time structure of insulin secretion by multiple parameter deconvolution analysis utilizing dog-specific insulin half-lives. RESULTS: Fasting plasma glucose concentrations in each group were similar, but all surgical groups were hyperglycemic with IV glucose challenge. Secretory pulse amplitude was decreased with decreased beta cell mass (PPX), partially normalized with systemic insulin release (SC), and further normalized with denervation (PAT). Interpulse interval and pulse duration were increased in all surgical groups when stimulated. Denervation of PAT resulted in a threefold increase in fasting basal invariant insulin secretion. Stimulated basal insulin secretion is inconsequential. CONCLUSIONS: Hyperinsulinemia and apparent insulin insensitivity after pancreas transplantation may be due to increased less potent basal secretion in the fasting state and less frequent, less discrete pulsatile insulin secretion in the simulated state.
Animals↗
Spatial proteomic mapping of the human and mouse retina using IBEX.
We generated a comparative spatial proteomic atlas of the human and mouse retina using a highly multiplexed immunohistochemistry technique called iterative bleaching extends multiplexity (IBEX). We refined the IBEX workflow by integrating an antibody dissociation option alongside chemical bleaching. This dual strategy enabled removal of the entire antibody complex, permitting the flexible use of antibodies from the same host species across iterative cycles. We coupled this workflow with super-resolution imaging via deconvolution and applied it to the retina of healthy humans and WT mice and the Crb1rd8 mouse model. We successfully imaged over 25 protein markers on human and mouse tissue sections, generating spatial atlases of the major retinal cell populations. Cross-species protein expression was compared to scRNA-seq datasets to identify protein and transcript disparities. Super-resolution IBEX delineated the ultrastructural features of the outer limiting membrane (OLM), identifying CD44 as a core structural component tightly colocalized with a highly organized F-actin belt within Müller glial endfeet. Using the Crb1rd8 mouse model, disruption of this complex was spatially associated with rosette formation and OLM structural failure. In summary, spatial proteomic atlases of the human and mouse retina were used to reveal insights into the arrangement of major retinal cell populations and OLM structure.
Animals↗
Connexin-specific distribution within gap junctions revealed in living cells.
To study the organization of gap junctions in living cells, the connexin isotypes alpha(1)(Cx43), beta(1)(Cx32) and beta(2)(Cx26) were tagged with the autofluorescent tracer green fluorescent protein (GFP) and its cyan (CFP) and yellow (YFP) color variants. The cellular fate of the tagged connexins was followed by high-resolution fluorescence deconvolution microscopy and time-lapse imaging. Comprehensive analyses demonstrated that the tagged channels were functional as monitored by dye transfer, even under conditions where the channels were assembled solely from tagged connexins. High-resolution images revealed a detailed structural organization, and volume reconstructions provided a three-dimensional view of entire gap junction plaques. Specifically, deconvolved dual-color images of gap junction plaques assembled from CFP- and YFP-tagged connexins revealed that different connexin isotypes gathered within the same plaques. Connexins either codistributed homogeneously throughout the plaque, or each connexin isotype segregated into well-separated domains. The studies demonstrate that the mode of channel distribution strictly depends on the connexin isotypes. Based on previous studies on the synthesis and assembly of connexins I suggest that channel distribution is regulated by intrinsic connexin isotype specific signals.
3T3 Cells↗
Use of evolutionary factor analysis in the spectroelectrochemistry of Escherichia coli sulfite reductase hemoprotein and a Mo/Fe/S cluster.
The deconvolution of spectroelectrochemical data is often quite difficult if the spectra of intermediates are not known. Factor analysis, however, has been shown to be a powerful technique which can make it possible to deconvolute overlapping spectra. In this work, evolving factor analysis will be used to determine the number of intermediates and the spectra of those species for two typical spectroelectrochemical experiments: linear scan voltammetry and chronoabsorptometry in a thin-layer cell. The first system was the reduction of E. coli sulfite reductase hemoprotein (SiR-HP). Principal factor analysis indicated that three species were present. By using evolving factor analysis, the potential regions where each of the species were present were identified, and their concentrations and spectra were determined by the use of the mass balance equation. The spectra of the one-electron (SiR-HP1-) and two-electron (SiR-HP2-) reduced product were compared with previous work. The second experiment was the chronoabsorptometry of Cl2FeS2MoS2FeCl2(2-) in methylene chloride. This experiment indicated that five species were present during the experiment. The entire set of 61 spectra were fit by assuming that there were 4 species present during the electrolysis. The rate constant for the appearance of subsequent species fit quite well with the rate constant for the disappearance of previous species. The spectra of the intermediates and final product were obtained using evolving factor analysis and a mass balance equation. Identification of the fifth species, which was probably the initial reduction product, Cl2FeS2MoS2FeCl2(3-), was difficult due to its low concentration and the fact that it was present in the same time region as the starting material.
Bacterial Proteins↗
Three-dimensional distribution of ryanodine receptor clusters in cardiac myocytes.
The clustering of ryanodine receptors (RyR2) into functional Ca2+ release units is central to current models for cardiac excitation-contraction (E-C) coupling. Using immunolabeling and confocal microscopy, we have analyzed the distribution of RyR2 clusters in rat and ventricular atrial myocytes. The resolution of the three-dimensional structure was improved by a novel transverse sectioning method as well as digital deconvolution. In contrast to earlier reports, the mean RyR2 cluster transverse spacing was measured 1.05 microm in ventricular myocytes and estimated 0.97 microm in atrial myocytes. Intercalated RyR2 clusters were found interspersed between the Z-disks on the cell periphery but absent in the interior, forming double rows flanking the local Z-disks on the surface. The longitudinal spacing between the adjacent rows of RyR2 clusters on the Z-disks was measured to have a mean value of 1.87 microm in ventricular and 1.69 microm in atrial myocytes. The measured RyR2 cluster distribution is compatible with models of Ca2+ wave generation. The size of the typical RyR2 cluster was close to 250 nm, and this suggests that approximately 100 RyR2s might be present in a cluster. The importance of cluster size and three-dimensional spacing for current E-C coupling models is discussed.
Animals↗
Comparison of wide-field/deconvolution and confocal microscopy in bioengineering. Interest of multi-photon microscopy in the study of articular cartilage.
The increase in lateral and spatial resolutions is one of the major targets of research and development in the field of optical microscopies applied to living tissue. The optical geometry of Confocal Laser Scanning Microscopy (CLSM) demonstrates its undeniable advantage on conventional fluorescence microscopy by segregating the planes outside the focussing plane. The methodological and technological advances of the last five years have been fast evolving, especially with regard to the optimisation of CLSM and deconvolution process. The limited analysis in thick tissue have given rise to the development of other techniques, multi-photon excitation microscopy in particular. In this paper, we have applied these techniques on major biological applications in bioengineering (endothelial cell, chondrocyte in 3D-culture, human cartilage) and discussed the technical limitations and perspectives.
Actins↗
Three-dimensional intracellular calcium gradients in single human burst-forming units-erythroid-derived erythroblasts induced by erythropoietin.
We have previously shown that the intracellular free Ca2+ increase induced by erythropoietin is likely related to differentiation rather than proliferation in human BFU-E-derived erythroblasts (1989. Blood. 73:1188-1194). Since cell differentiation involves transcription of specific regions of the genome, and since nuclear endonucleases responsible for single strand DNA breaks observed in cells undergoing differentiation are Ca2+ dependent, we investigated whether the erythropoietin-induced calcium signal is transmitted from cytosol to nucleus in this study. To elucidate subcellular Ca2+ gradients, the technique of optical sectioning microscopy was used. After determining the empirical three-dimensional point spread function of the video imaging system, contaminating light signals from optical planes above and below the focal plane of interest were removed by deconvolution using the nearest neighboring approach. Processed images did not reveal any discernible subcellular Ca2+ gradients in unstimulated erythroblasts. By contrast, with erythropoietin stimulation, there was a two- to threefold higher Ca2+ concentration in the nucleus compared to the surrounding cytoplasm. We suggest that the rise in nuclear Ca2+ may activate Ca2(+)-dependent endonucleases and initiate differentiation. The approach described here offers the opportunity to follow subcellular Ca2+ changes in response to a wide range of stimuli, allowing new insights into the role of regional Ca2+ changes in regulation of cell function.
Calcium↗
Actin dynamics coupled to clathrin-coated vesicle formation at the trans-Golgi network.
In diverse species, actin assembly facilitates clathrin-coated vesicle (CCV) formation during endocytosis. This role might be an adaptation specific to the unique environment at the cell cortex, or it might be fundamental, facilitating CCV formation on different membranes. Proteins of the Sla2p/Hip1R family bind to actin and clathrin at endocytic sites in yeast and mammals. We hypothesized that Hip1R might also coordinate actin assembly with clathrin budding at the trans-Golgi network (TGN). Using deconvolution and time-lapse microscopy, we showed that Hip1R is present on CCVs emerging from the TGN. These vesicles contain the mannose 6-phosphate receptor involved in targeting proteins to the lysosome, and the actin nucleating Arp2/3 complex. Silencing of Hip1R expression by RNAi resulted in disruption of Golgi organization and accumulation of F-actin structures associated with CCVs on the TGN. Hip1R silencing and actin poisons slowed cathepsin D exit from the TGN. These studies establish roles for Hip1R and actin in CCV budding from the TGN for lysosome biogenesis.
Actins↗
Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces.
Mechanisms of bacterial pathogenesis have become an increasingly important subject as pathogens have become increasingly resistant to current antibiotics. The adhesion of microorganisms to the surface of host tissue is often a first step in pathogenesis and is a plausible target for new antiinfective agents. Examination of bacterial adhesion has been difficult both because it is polyvalent and because bacterial adhesins often recognize more than one type of cell-surface molecule. This paper describes an experimental procedure that measures the forces of adhesion resulting from the interaction of uropathogenic Escherichia coli to molecularly well defined models of cellular surfaces. This procedure uses self-assembled monolayers (SAMs) to model the surface of epithelial cells and optical tweezers to manipulate the bacteria. Optical tweezers orient the bacteria relative to the surface and, thus, limit the number of points of attachment (that is, the valency of attachment). Using this combination, it was possible to quantify the force required to break a single interaction between pilus and mannose groups linked to the SAM. These results demonstrate the deconvolution and characterization of complicated events in microbial adhesion in terms of specific molecular interactions. They also suggest that the combination of optical tweezers and appropriately functionalized SAMs is a uniquely synergistic system with which to study polyvalent adhesion of bacteria to biologically relevant surfaces and with which to screen for inhibitors of this adhesion.
Bacterial Adhesion↗
A protocol for 3D image reconstruction from a single image of an oblique section.
Oblique section 3D reconstruction can produce a 3D image of a sectioned crystal from a single electron micrograph. We describe here in detail a reconstruction protocol applicable to an electron micrograph of an oblique section through a 3D crystal. The protocol is described in six steps: (1) selection criteria for images, (2) preprocessing steps to correct for image defects, (3) determination of unit cell coordinates, (4) interpolation of strip images with correction for image distortions and crystal disorder, (5) production of a crystallographic serial section reconstruction, (6) correction for skewed sampling to produce an oblique section reconstruction. In addition, we explore Wiener filter deconvolution of the section thickness. We describe a method for determining the section thickness by comparing data from projections of the oblique section reconstruction with corresponding data from a thick longitudinal section. Several schemes for Wiener filter deconvolution are described that differ in the way information on the signal-to-noise ratio is used in the filter.
Animals↗
A nuclear magnetic resonance imaging technique designed for studies of water in plant leaves.
A new imaging technique is described which uses nuclear magnetic resonance (NMR) to create a water profile of plant leaves. The water profile shows the average distribution of water as a function of depth into a leaf along a line perpendicular to the leaf surface; it can be used to measure the thickness of cell layers and the quantity of water in each layer. Two-dimensional NMR methods were used to avoid chemical shift distortion which degrades the resolution in leaf images made by conventional NMR techniques; image resolution was improved further by deconvolution analysis. To illustrate its application, the technique was used to follow changes in the internal structure of developing leaves.
Evaluation Studies as Topic↗
Structure and conformational stability of the enzyme I of Streptomyces coelicolor explored by FTIR and circular dichroism.
The bacterial phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS), formed by a cascade of several proteins, couples the translocation and phosphorylation of specific sugars across cell membranes. The structure and thermal stability of the first protein (enzyme I, EI) of the PTS in Streptomyces coelicolor is studied by using far-UV circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) at pH 7.0. The deconvolution of FTIR spectra indicates that the protein is mainly composed by a 35% of alpha-helical structure and 30% of beta-sheet. The thermal denaturation curves, as followed by both techniques, show only a midpoint at 330 K. This thermal denaturation behaviour is different to that observed in other members of the EI family.
Bacterial Proteins↗
PNA-encoded protease substrate microarrays.
Our current understanding of the role and regulation of protease activity in normal and pathogenic processes is limited by our ability to measure and deconvolute their enzymatic activity. To address this limitation, an approach was developed that utilizes rhodamine-based fluorogenic substrates encoded with PNA tags. The PNA tags address each of the substrates to a predefined location on an oligonucleotide microarray through hybridization, thus allowing the deconvolution of multiple signals from a solution. A library of 192 protease substrates was prepared by split and mix combinatorial synthesis. The methodology and validation of this approach for profiling proteolytic activity from single proteases and from those in crude cell lysates as well as clinical blood samples is described.
Humans↗
Tubulin secondary structure analysis, limited proteolysis sites, and homology to FtsZ.
The far-ultraviolet circular dichroism spectrum of the alpha beta-tubulin dimer analyzed by six different methods indicates an average content of approximately 33% alpha helix, 21% beta sheet, and 45% other secondary structure. Deconvolution of Fourier transform infrared spectra indicates 24% sheet, 37% (maximum) helix, and 38% (minimum) other structure. Separate alignments of 75 alpha-tubulin, 106 beta-tubulin, and 14 gamma-tubulin sequences and 12 sequences of the bacterial cell division protein FtsZ have been employed to predict their secondary structures with the multiple-sequence method PHD [Rost, B., & Sander, C. (1993a) J. Mol. Biol. 232, 584-599]. The predicted secondary structures average of 33% alpha helix, 24% beta sheet, and 43% loop for the alpha beta dimer. The predictions have been compared with sites of limited proteolysis by 12 proteases at the surfaces of the heterodimer and taxol-induced microtubules [de Pereda, J. M., & Andreu, J. M. (1996) Biochemistry 35, 14184-14202]. From 24 experimentally determined nicking sites, 18 are at predicted loops or at the extremes of secondary structure elements. Proteolysis zone A (including acetylable Lys40 and probably Lys60 in alpha-tubulin and Gly93 in beta-tubulin) and proteolysis zone B (extending between residues 167 and 183 in both chains) are accessible in microtubules. Proteolysis zone C, between residues 278 and 295, becomes partially occluded in microtubules. The alpha-tubulin nicking site Arg339-Ser340 is at a loop following a predicted alpha helix in proteolysis zone D. This site is protected in taxol microtubules; however, a new tryptic site appears which is probably located at the N-terminal end of the same helix. Zone D also contains beta-tubulin Cys354, which is accessible in microtubules. Proteolysis zone E includes the C-terminal hypervariable loops (10-20 residues) of each tubulin chain. These follow the two larger predicted helical zones (residues 372-395 and 405-432 in beta-tubulin), which also are the longer conserved part of the alpha- and beta-tubulin sequences. Through combination of this with other biochemical information, a set of surface and distance constraints is proposed for the folding of beta-tubulin. The FtsZ sequences are only 10-18% identical to the tubulin sequences. However, the predicted secondary structures show two clearly similar (85-87 and 51-78%) regions, at tubulin positions 95-175 and 305-350, corresponding to FtsZ 65-135 and 255-300, respectively. The first region is flanked by tubulin proteolysis zones A and B. It consists of a predicted loop1-helix-loop2-sheet-loop3-helix-loop4-sheet fold, which contains the motif (KR)GXXXXG (loop1), and the tubulin-FtsZ signature G-box motif (SAG)GGTG(SAT)G (loop3). A simple working model envisages loop1 and loop3 together at the nucleotide binding site, while loops 2 and 4 are at the surface of the protein, in agreement with proteolytic and antigenic accessibility results in tubulin. The model is compatible with studies of tubulin and FtsZ mutants. It is proposed that this region constitutes a common structural and evolutionary nucleus of tubulins and FtsZ which is different from typical GTPases.
Amino Acid Sequence↗