Profile matching and profile subtraction: application of computer-based image analysis system for two-dimensional electrophoresis gels

The microcomputer-based image analysis system IB-1000 (developed by Indiana Biotech, Highland, IN) for two-dimensional electrophoresis gels has been described previously (9). It allows the user to compare protein spots between two profiles and identify those spots that are commonly shared in both profiles. This report describes two applications of the system's global comparison routine-profile matching and profile subtraction. This application is able to subtract commonly shared spots from one profile, creating a new profile made up by the unmatched spots in the other profile. These applications can be employed in a large variety of research projects.     

The <Emphasis Type="Italic">Arabidopsis</Emphasis> calmodulin-like proteins AtCML30 and AtCML3 are targeted to mitochondria and peroxisomes,respectively

Calmodulin (CaM) is a ubiquitous sensor/transducer of calcium signals in eukaryotic organisms. While CaM mediated calcium regulation of cytosolic processes is well established, there is growing evidence for the inclusion of organelles such as chloroplasts, mitochondria and peroxisomes into the calcium/calmodulin regulation network. A number of CaM-binding proteins have been identified in these organelles and processes such as protein import into chloroplasts and mitochondria have been shown to be governed by CaM regulation. What have been missing to date are the mediators of this regulation since no CaM or calmodulin-like protein (CML) has been identified in any of these organelles. Here we show that two Arabidopsis CMLs, AtCML3 and AtCML30, are localized in peroxisomes and mitochondria, respectively. AtCML3 is targeted via an unusual C-terminal PTS1-like tripeptide while AtCML30 utilizes an N-terminal, non-cleavable transit peptide. Both proteins possess the typical structure of CaMs, with two pairs of EF-hand motifs separated by a short linker domain. They furthermore display common characteristics, such as calcium-dependent alteration of gel mobility and calcium-dependent exposure of a hydrophobic surface. This indicates that they can function in a similar manner as canonical CaMs. The presence of close homologues to AtCML3 and AtCML30 in other plants further indicates that organellar targeting of these CMLs is not a specific feature of Arabidopsis. The identification of peroxisomal and mitochondrial CMLs is an important step in the understanding how these organelles are integrated into the cellular calcium/calmodulin signaling pathways.     

Mitochondria and hydrogenosomes are two forms of the same fundamental organelle

Published data suggest that hydrogenosomes, organelles found in diverse anaerobic eukaryotes that make energy and hydrogen, were once mitochondria. As hydrogenosomes generally lack a genome, the conversion is probably one way. The sources of the key hydrogenosomal enzymes, pyruvate : ferredoxin oxidoreductase (PFO) and hydrogenase, are not resolved by current phylogenetic analyses, but it is likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobic eukaryotes, the proteins are intimately integrated into the fabric of diverse eukaryotic cells, where they are targeted to different cell compartments, and not just hydrogenosomes. There is no evidence supporting the view that PFO and hydrogenase originated from the mitochondrial endosymbiont, as posited by the hydrogen hypothesis for eukaryogenesis. Other organelles derived from mitochondria have now been described in anaerobic and parasitic microbial eukaryotes, including species that were once thought to have diverged before the mitochondrial symbiosis. It thus seems possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, to which different types of biochemistry can be targeted. It remains to be seen if, despite their obvious differences, this family of organelles shares a common function of importance for the eukaryotic cell, other than energy production, that might provide the underlying selection pressure for organelle retention.     

Calcium regulation in endosymbiotic organelles of plants

In plant cells calcium-dependent signaling pathways are involved in a large array of biological processes in response to hormones, biotic/abiotic stress signals and a variety of developmental cues. This is generally achieved through binding of calcium to diverse calcium-sensing proteins, which subsequently control downstream events by activating or inhibiting biochemical reactions. Regulation by calcium is considered as a eukaryotic trait and has not been described for prokaryotes. Nevertheless, there is increasing evidence indicating that organelles of prokaryotic origin, such as chloroplasts and mitochondria, are integrated into the calcium-signaling network of the cell. An important transducer of calcium in these organelles appears to be calmodulin. In this review we want to give an overview over present data showing that endosymbiotic organelles harbour calcium-dependent biological processes with a focus on calmodulin-regulation.Key words: mitochondria, chloroplasts, calcium, calmodulin, EF-hand proteins     

Does sulphide detoxication occur in the gills of the hydrothermal vent shrimp, Rimicaris exoculata?Y a-t-il détoxication des sulfures dans les branchies de la crevette hydrothermale, Rimicaris exoculata ?

Ultrastructural observations of the gills of the hydrothermal vent shrimp Rimicaris exoculata reveal that the epithelial cells contain numerous mitochondria clustered around unusual organelles (diameter of 0.7 to 2.5 microns) containing membrane stacks. These organelles were termed sulphide-oxidising bodies (SOBs) by structural analogy with organelles observed in the tissues of species adapted to sulphide-rich environments. Moreover, in the gills of R. exoculata, mitochondria display numerous electron-dense granules in their stroma. Such ultrastructural features suggest that sulphide detoxication may probably occur in the gills of R. exoculata. Comparable structures were also described in the gills of other hydrothermal vent species, as the alvinellid Pompeii worms that, as R. exoculata, are housing ectosymbiotic bacteria.     

Cognate peptide-receptor ligand mapping by directed phage display

Background  

A rapid phage display method for the elucidation of cognate peptide specific ligand for receptors is described. The approach may be readily integrated into the interface of genomic and proteomic studies to identify biologically relevant ligands.     

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.     

Theoretical approaches for understanding the self-organized formation of the Golgi apparatus

Eukaryotic cells fold their membranes into highly organized structures called membrane-bound organelles. Organelles display characteristic structures and perform specialized functions related to their structures. Focusing on the Golgi apparatus, we provide an overview of recent theoretical studies to explain the mechanism of the architecture of the Golgi apparatus. These studies are classified into two categories: those that use equilibrium models to describe the robust Golgi morphology and those that use non-equilibrium models to explain the stationarity of the Golgi structures and the constant streaming of membrane traffic. A combinational model of both categories was used for computational reconstruction of the de novo Golgi formation process, which might provide an insight into the integrated understanding of the Golgi structure.     

Formaldehyde-induced appearance of septate junctions between digestive vacuoles

Tissue biopsies from (1) some chronic inflammatory diseases, (2) a necrotic tumoral process, (3) normal human lymphatic ganglia, and (4) two congenital diseases of the adrenal cortex were selected for study. A block from each biopsy was fixed in glutaraldehyde-paraformaldehyde; a second block was fixed in 10% formaldehyde. In all cases septate junctions between digestive vacuoles did occur in phagocytic cells and some adrenal cortex cells fixed in formaldehyde. These junctions were similar to those reported recently for malakoplakia phagocytes. Consistently, they were not found to attach organelles other than lysosomes derivatives. Both phagocytes and adrenal cortex cells in the material fixed in glutaraldehyde-paraformaldehyde did not display adhesive specializations between digestive vacuoles. This suggests that the septate junctions described herein are artifactuous structures induced by formaldehyde. There is, however, a certain degree of specificity of cells having the capability of developing these septate junctions. It is assumed that the coating material of digestive organelles in phogocytes and some other cells would be responsible for both cell specificity and organelle specificity of the formaldehyde-induced septate junctions.     

Autophagy and the integrated stress response

Autophagy is a tightly regulated pathway involving the lysosomal degradation of cytoplasmic organelles or cytosolic components. This pathway can be stimulated by multiple forms of cellular stress, including nutrient or growth factor deprivation, hypoxia, reactive oxygen species, DNA damage, protein aggregates, damaged organelles, or intracellular pathogens. Both specific, stimulus-dependent and more general, stimulus-independent signaling pathways are activated to coordinate different phases of autophagy. Autophagy can be integrated with other cellular stress responses through parallel stimulation of autophagy and other stress responses by specific stress stimuli, through dual regulation of autophagy and other stress responses by multifunctional stress signaling molecules, and/or through mutual control of autophagy and other stress responses. Thus, autophagy is a cell biological process that is a central component of the integrated stress response.     

Peroxisome biogenesis

Peroxisomes are eukaryotic organelles that are the subcellular location of important metabolic reactions. In humans, defects in the organelle's function are often lethal. Yet, relative to other organelles, little is known about how cells maintain and propagate peroxisomes or how they direct specific sets of newly synthesized proteins to these organelles (peroxisome biogenesis/assembly). In recent years, substantial progress has been made in elucidating aspects of peroxisome biogenesis and in identifying PEX genes whose products, peroxins, are essential for one or more of these processes. The most progress has been made in understanding the mechanism by which peroxisome matrix proteins are imported into the organelles. Signal sequences responsible for targeting proteins to the organelle have been defined. Potential signal receptor proteins, a receptor docking protein and other components of the import machinery have been identified, along with insights into how they operate. These studies indicate that multiple peroxisomal protein-import mechanisms exist and that these mechanisms are novel, not simply variations of those described for other organelles.     

bcd: A mutation affecting the width of organelle domains in the cortex of Tetrahymena thermophila

Summary A single-gene recessive mutation, bcd (broadened cortical domains), of Tetrahymena thermophila is characterized by a variable broadening of the spatial domains within which cortical organelles, including both the contractile vacuole pores (CVP) and oral apparatus (OA), are formed. The phenotype is not temperature-sensitive. During the development of the organelles of the mutant prior to cell division, extra CVPs and extra oral primordia (OP) appear near ciliary rows adjacent to the rows at which these structures normally form. In the later stages of development, some, but not all, of these extra structures are resorbed, or in the case of the oral domain, multiple adjacent OPs may be completely or partially integrated into a single enlarged OA. When multiple OAs persist, one or more of these may display a reversed orientation reminiscent of those encountered in janus mutants. However, unlike janus, bcd cells do not express any sign of a mirror-image global organization.Our results can best be accounted for by postulating that the bcd mutation affects some common determinant of the widths of both CVP and OA domains. Studies are in progress which explore the relationship between this width-determining mechanism(s) and the mechanism(s) determining the location of cortical organelles around the cell circumference.     

Interactive map projection algorithm for illustrating protein surfaces

An interactive map projection algorithm and cluster analysis program are described which can be used in the display and analysis of protein surfaces. The application of the techniques to the analysis of protein charge distributions is described, and a brief discussion presented on various other applications.     

The transport of organelles in axons

The fast anterograde and retrograde transport systems in axons convey organelles from the soma, where synthesis occurs, to the synaptic region and back. Studies of label incorporation into newly synthesized organelles show that they move along the axon with profiles resembling traveling waves. The underlying mechanism appears to be that cross-bridging “engines” attach to the organelles and this complex then attaches by the engines to the surface of microtubules, resulting in translocation of the organelles. A model incorporating this mechanism predicts traveling-wave-like profiles of labeled organelles and can serve to link mechanistic information with fast transport measurements in intact axons. Analysis of the simplest case provides insight into the factors determining the speed and shape of the wavelike profile.     

A mammary gland whole mount technique that preserves cell fine structure for electron miscroscopy.

A mammary gland whole mount technique has been developed that preserves cell fine structure and makes it possible to also examine the preparations by electron microscopy. The glands are placed on glass microscope slides, fixed in a paraformaldehyde-glutaraldehyde mixture, defatted in acetone, stained with 0.5% methylene blue (or trypan blue) in saline, and dehydrated in ethanol. They are evaluated and photographed in 100% ethanol. Then specific areas (i.e. containing small growths, tumors, or other lesions) are selected, excised and prepared for electroscopy. The ultrastructural preservation is good, organelles are evident and there is no observable dye precipitate. The only unusual finding is that cell membranes display a "negative" image.     

Analysis of confocal images using variable-width line profiles

A line profile of fluorescent intensities in confocal images is frequently examined. We have developed the computer software tool to analyse the profiles of intensities of fluorescent probes in confocal images. The software averages neighbouring pixels, adjacent to the central line, without reducing the spatial resolution of the image. As an experimental model, we have used the skeletal muscle fibre isolated from the rat skeletal muscle extensor digitorum brevis. As a marker of myofibrils' structure, we have used phalloidin–rhodamine staining and the anti-TIM antibody to label mitochondria. We also tested the distribution of the protein kinase B/Akt. Since signalling is ordered in modules and large protein complexes appear to direct signalling to organelles and regulate specific physiological functions, a software tool to analyse such complexes in fluorescent confocal images is required. The software displays the image, and the user defines the line for analysis. The image is rotated by the angle of the line. The line profile is calculated by averaging one dimension of the cropped rotated image matrix. The spatial resolution in averaged line profile is not decreased compared with single-pixel line profile, which was confirmed by the discrete Fourier transform computed with a fast Fourier transform algorithm. We conclude that the custom software tool presented here is a useful tool to analyse line profiles of fluorescence intensities in confocal images.     

Septate junctions between digestive vacuoles in human malacoplakia

Typical septate junctions between digestive vacuoles in phagocytic cells of human malacoplakia are described in this paper. Evidence for a honeycomb pattern of hexagonal subunits is presented for their cleft material. Junctions were not observed between other organelles or in cells other than phagocytes. It is assumed that the septate junctions described here may reflect a pathological change in the organization of the membrane components of digestive organelles.     

On the Fine Structure of Valvognathia pogonostoma gen. et sp.n. (Gnathostomulida, Onychognathiidae) with Special Reference to the Jaw Apparatus

Valvognathia pogonostoma gen. et sp.n. is described as belonging to the family Onychognathiidae Sterrer, 1972. An integrated picture of the jaw apparatus is presented, based on interference phase contrast (Nomarski) and electron microscopy. The teeth are shown to be continuous with lamellae, apophyses, fibulae, and even jugum. These structures are all extracellular secretions covering the apical surfaces of the jaw apparatus epithelium. They constitute a single, interconnected, "cuticular" structure. Spiral-ciliary-organs and rhabditoid organelles are described in the epidermis.     

INVITED SPECIAL PAPER: The hows and whys of cytoplasmic inheritance in seed plants

Cytoplasmic organelles are inherited in a nonMendelian fashion in all eukaryotic organisms investigated. Among the seed plants, plastids can be inherited strictly from the female parent, strictly from the male parent, or biparentally. Most flowering plants studied to date exhibit maternal plastid inheritance, but approximately one-third of the genera investigated display biparental plastid inheritance to some degree. Among the gymnosperms, paternal plastid inheritance is the rule in the conifers, whereas the other groups appear to have maternal plastid inheritance, although they have been less well studied. Mitochondrial inheritance is predominantly maternal in the seed plants, except for a few coniferous families where it is predominantly paternal. The advent of recombinant DNA technology has allowed restriction fragment length polymorphisms to be used as molecular markers, and has stimulated much research in organelle inheritance and its application to studies of population genetics and phylogenetic biology. This report emphasizes the various mechanisms by which organelles are, or are not, transmitted among the seed plants in order that researchers directly or indirectly involved with organelle inheritance may better understand the potential and the limitations of their investigations. A summary and discussion of the possible evolutionary significance of the various patterns of cytoplasmic inheritance among the seed plants are also included.