Biomedical subjects

E Kellenberger

Publications and source records attributed to E Kellenberger.

At least 19 recordsLinked to original sources

PubMed1998

Alpha-helix mimicry of a beta-turn.

It is shown here that the three-dimensional arrangement of the amino acids in an RGDF beta-turn (sequence involved in cell adhesion) resembles that of an alpha-helix with a shuffled RGDF sequence (i.e. RGXFD). A miniprotein was designed and constructed which arranges the RGXFD sequence into a well defined helical conformation. The designed protein is bioactive and folds into the desired structure as assessed by nuclear magnetic resonance spectroscopy. The recognition process mediated by a beta-turn can thus be mimicked by an alpha-helix.

Amino Acid Sequence↗

PubMed1998

Learning about truth and biases through experience: section surface corrugation, protein denaturation, and staining.

By developing and investigating the use of thin resin sections for electron microscopy, we discovered that many of the current biases became invalid: 1) No evidence could be produced that the involved organic liquids produce the protein denaturation responsible for loss of antigenicity and lowered resolution. For immunolabeling, "water-soluble" resins are not per se to be preferred over less polar and more hydrophobic ones. 2) The relief formed by the corrugated section surface enables access to the antigenic sites. The depth of relief is determined by the strength of copolymerization and depends on temperature, the chemical nature of resin and biological matter, and, thus, also on surface modification through fixatives. The stronger the relief, the better the immunolabeling and the less the image resolution. Strong copolymerization favors flatter relief, but also a hiding of antigenic sites by thin layers of resin. 3) Heavy metal stain remains the main culprit for low resolution of sections when compared to results obtained with other preparation methods.

Image Enhancement↗

PubMed1996

Mechanism of the long tail-fiber deployment of bacteriophages T-even and its role in adsorption, infection and sedimentation.

Models for the tail-fiber deployment of T-even bacteriophages have been experimentally tested by correlating sedimentation constants, adsorption rates, protease inactivation kinetics, and fiber configurations of individual phages observed by electron microscopy. Neither the collective nor the individualistic model, i.e. coordinated fiber retraction and expansion or oscillation of fibers independently of each other, respectively, could satisfactorily account for the results presented. We propose a new intermediary model, in which the base-plate determines a collective behaviour by fixing the hinge angle, around which individual fibers oscillate freely. The bidisperse, so-called dual sedimentation was shown to occur mainly with nascent high-concentration phage stocks in potassium glutamate containing media. Indeed, when mature intracellular phages are released in 0.5 M potassium glutamate--a condition simulating the intracellular environment--only the fast form appears. Upon storage in the cold or release into 0.5 M chloride, both forms appear. Results confirming that the sedimentation constants of the fast and slow form roughly correspond to those of the monodisperse sedimentation, characteristic of the extreme pH values, i.e. 5 and 8, do not allow to conclude that fiber configuration is the only cause of the bidisperse sedimentation.

Adsorption↗

PubMed1995

Electron microscopic studies on intracellular phage development--history and perspectives.

This review is centered on the applications of thin sections to the study of intracellular precursors of bacteriophage heads. Results obtained with other preparation methods are included in so far as they are essential for the comprehension of the biological problems. This type of work was pioneered with phage T4, which contributed much to today's understanding of morphogenesis and form determination. The T4 story is rich in successes, but also in many fallacies. Due to its large size, T4 is obviously prone to preparation artefacts such as emptying, flattening and others. Many of these artefacts were first encountered in T4. Artefacts are mostly found in lysates, however, experience shows that they are not completely absent from thin sections. This can be explained by the fact that permeability changes induced by fixatives occur. The information gained from T4 was profitably used for the study of other phages. They are included in this review as far as electron microscopic studies played a major role in the elucidation of their morphogenetic pathways. Research on phage assembly pathways and form determination is a beautiful illustration for the power of the integrated approach which combines electron microscopy with biochemistry, genetics and biophysics. As a consequence, we did not restrict ourselves to the review of electron microscopic work but tried to integrate pertinent data which contribute to the understanding of the molecular mechanisms acting in determining the form of supramolecular structures.

Artifacts↗

PubMed1995

Induction of complex intracytoplasmic membranes related to nitrogen fixation in Azoarcus sp. BH72.

We report the discovery of novel subcellular structures related to bacterial nitrogen fixation in the strictly respiratory diazotrophic bacterium Azoarcus sp. BH72, which was isolated as an endophyte from Kallar grass. Nitrogenase is derepressed under microaerobic conditions at O2 concentrations in the micromolar range. With increasing O2 deprivation, bacteria can develop into a hyperinduced state, which is characterized by high specific rates of respiration and efficient nitrogen fixation at approximately 30 nM O2. Ultrastructural analysis of cells in the course of hyperinduction revealed that complex intracytoplasmic membrane systems are formed, which consist of stacks of membranes and which are absent under standard nitrogen-fixing conditions. The iron protein of nitrogenase was highly enriched on these membranes, as evidenced by immunohistochemical studies. Membrane deficiency in NifH/K- mutants, a deletion mutant in the nifK gene and the character of NH+4-grown cells suggested, in concert with the membrane localization of nitrogenase, that these structures are specialized membranes related to nitrogen fixation. We propose the term 'diazosomes' for them. Development of intracytoplasmic membranes coincides with the appearance of a high-molecular-mass form of the iron protein of nitrogenase, which was detectable in membrane fractions. Mutational analysis, and determination of the N-terminal amino acid sequence indicate that the nifH gene product is covalently modified by a mechanism probably different from adenosine diphosphoribosylation. Development of diazosomes in nitrogen-fixing cells can be induced in pure cultures and in co-culture with a fungus isolated from the rhizosphere of Kallar grass.

Blotting, Western↗

PubMed1994

Genetic ecology: a new interdisciplinary science, fundamental for evolution, biodiversity and biosafety evaluations.

Genetic ecology is the extension of our modern knowledge in molecular genetics to studies of viability, gene expression and gene movements in natural environments like soils, aquifers and digestive tracts. In such milieux, the horizontal transfer of plasmid-borne genes between phylogenetically distant species has already been found to be much more frequent than had been expected from laboratory experience. For the study of exchanges involving chromosomally-located genes, more has to be learned about the behaviour of transposons in such environments. The results expected from studies in genetic ecology are relevant for considerations of evolution, biodiversity and biosafety. The role of this new field of research in restoring popular confidence in science and in its biotechnological applications is stressed.

Animals↗

PubMed1994

Unstained and in vivo fluorescently stained bacterial nucleoids and plasmolysis observed by a new specimen preparation method for high-power light microscopy of metabolically active cells.

Microscope slides were coated with a layer of gelatin, the thickness of the gelatin increasing linearly along the long axis. The bacterial suspension is applied to the dried gelatin and covered by a coverslip. The medium is absorbed by the gelatin and thus the cells applied against the coverslip. By this method, cultures of concentrations below 10(8) cells/ml provide statistically relevant numbers for observation without prior concentration steps. It is easier to apply than the existing methods for the observation of bacterial nucleoids by phase contrast imaging. Because the cells are maintained in growing conditions the method is useful for the vital fluorescence DAPI-staining of various bacterial species and for observations of plasmolysis and its reversal at different physiological conditions and extracellular osmolalities. The previously generally assumed view that the plasmolytic changes of the cell morphology are immediate upon the hyperosmotic shock and are rapidly repaired when the cell is able to metabolize actively was confirmed; this is in contrast to some recent claims.

Bacillus↗

PubMed1994

Root colonization and systemic spreading of Azoarcus sp. strain BH72 in grasses.

The invasive properties of Azoarcus sp. strain BH72, an endorhizospheric isolate of Kallar grass, on gnotobiotically grown seedlings of Oryza sativa IR36 and Leptochloa fusca (L.) Kunth were studied. Additionally, Azoarcus spp. were localized in roots of field-grown Kallar grass. To facilitate localization and to assure identity of bacteria, genetically engineered microorganisms expressing beta-glucuronidase were also used as inocula. beta-Glucuronidase staining indicated that the apical region of the root behind the meristem was the most intensively colonized. Light and electron microscopy showed that strain BH72 penetrated the rhizoplane preferentially in the zones of elongation and differentiation and colonized the root interior inter- and intracellularly. In addition to the root cortex, stelar tissue was also colonized; bacteria were found in the xylem. No evidence was obtained that Azoarcus spp. could reside in living plant cells; rather, plant cells were apparently destroyed after bacteria had penetrated the cell wall. A common pathogenicity test on tobacco leaves provided no evidence that representative strains of Azoarcus spp. are phytopathogenic. Compared with the control, inoculation with strain BH72 significantly promoted growth of rice seedlings. This effect was reversed when the plant medium was supplemented with malate (0.2 g/liter). N2 fixation was apparently not involved, because the same response was obtained with a nifK mutant of strain BH72, which has a Nif- phenotype. Also, Western blot (immunoblot) analysis of protein extracts from rice seedlings gave no indication that nitrogenase was present. PCR and Western immunoblotting, using primers specific for eubacteria and antibodies recognizing type-specific antigens, respectively, indicated that strain BH72 could colonize rice plants systemically, probably mediated by longitudinal spreading through vessels.

Antibodies, Bacterial↗

PubMed1994

The bacterial nucleoid revisited.

This review compares the results of different methods of investigating the morphology of nucleoids of bacteria grown under conditions favoring short generation times. We consider the evidence from fixed and stained specimens, from phase-contrast and fluorescence microscopy of growing bacteria, and from electron microscopy of whole as well as thinly sectioned ones. It is concluded that the nucleoid of growing cells is in a dynamic state: part of the chromatin is "pulled out" of the bulk of the nucleoid in order to be transcribed. This activity is performed by excrescences which extend far into the cytoplasm so as to reach the maximum of available ribosomes. Different means of fixation provide markedly different views of the texture of the DNA-containing plasm of the bulk of the nucleoid. Conventional chemical fixatives stabilize the cytoplasm of bacteria but not their protein-low chromatin. Uranyl acetate does cross-link the latter well but only if the cytoplasm has first been fixed conventionally. In the interval between the two fixations, the DNA arranges itself in liquid-crystalline form, supposedly because of loss of supercoiling. In stark contrast, cryofixation preserves bacterial chromatin in a finely granular form, believed to reflect its native strongly negatively supercoiled state. In dinoflagellates the DNA of their permanently visible chromosomes (also low in histone-like protein) is natively present as a liquid crystal. The arrangement of chromatin in Epulocystis fishelsoni, one of the largest known prokaryotes, is briefly described.

Animals↗

PubMed1994

Immunostaining of DNA in electron microscopy: an amplification and staining procedure for thin sections as alternative to gold labeling.

We describe a new electron microscopic on-section staining technique with high specificity and sensitivity for DNA-containing structures. Lowicryl HM20 sections of specimens obtained by cryofixation and freeze-substitution are incubated in a first step with a primary IgM antibody specific for double-stranded DNA. The layer of bound antibodies at the section surface is amplified in a successive step by a secondary IgG antibody. Finally, electron scattering of the antibody layer produced is enhanced by staining with a mixture of uranyl acetate and potassium permanganate. The applicability of the method is exemplified by the detection of shape and distribution of various types of bacterial and eukaryotic chromatin.

Animals↗

PubMed1993

The inactive form of recA protein: the 'compact' structure.

When recA protein is enzymatically inactive in vitro, it adopts a more compact helical polymer form than that of the active protein polymerized onto DNA in the presence of ATP. Here we describe some aspects of this structure. By cryo-electron microscopy, a pitch of 76 A is found for both the self-polymer and the inactive complex with ssDNA. A smaller pitch of 64 A is observed in conventional electron micrographs. The contour length of complexes with ssDNA was used to estimate the binding stoichiometry in the compact complex, 6 +/- 1 nt/recA. In addition, the compact structure was observed in vivo in Escherichia coli: inclusion bodies produced upon induction of recA expression in an overproducing strain have a fibrous morphology with the structural parameters of the compact polymer.

Bacteriophage T4↗

PubMed1993

Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM.

Quantitative STEM with the imaging mode of ratio-contrast was investigated in order to evaluate the local concentration of DNA in situ for different kinds of DNA plasms in terms of intracellular packing densities (p.d.). The ability of ratio imaging to suppress thickness variations provided the basis to use unstained sections from cryofixed and freeze-substituted material. The DNA p.d. within the nucleoid of E. coli was determined to be about 100 mg ml-1. Quantitative data concerning the p.d. of DNA in condensed eukaryotic chromatin assuming equal amounts of DNA and protein were evaluated for the first time: approximately 400 mg ml-1 chromatin which corresponds to 200 mg ml-1 DNA. The p.d. of DNA in chromosomes from the dinoflagellate Amphidinium carterae, a eukaryote devoid of histones and with only small relative amounts of histone-like protein, was also found to be of the order of 200 mg ml-1. The highest p.d. of DNA was measured for the head of the bacteriophage T4 with more than 800 mg ml-1, in fair agreement with previous calculations. The results provide further support for a condensation mode of low protein chromatins that involves a liquid-crystalline organization of the DNA filaments.

Animals↗

PubMed1992

Chromatins of low-protein content: special features of their compaction and condensation.

Histonic chromatin with a relatively high-protein content (RPC of about 1) is compared with naturally occurring chromatins of low-protein contents (RPCs of less than 0.5). The features of these chromatins, with respect to compaction and condensation, are discussed. Liquid crystalline chromatin, as found in dinoflagellates and phage heads, can apparently only be formed by condensation of chromatin of low-protein content and when it is not supercoiled. With histonic chromatin, liquid crystals are never found. Chromatins with low-protein contents might also form compactosomes (or 'labile nucleosomes'), as, for instance, in bacteria. They are forms of supercoiled DNA without a protein core and are so labile that they are difficult to study and even to detect. Chemical fixatives, as commonly used for electron microscopy, do not cross-link the chromatins of low-protein content, a feature which they share with naked DNA. It is postulated that these fixatives even relax the existing supercoil, which seems to be preserved after cryofixation only.

Chromatin↗

PubMed1992

Artefacts and morphological changes during chemical fixation.

The normally 'condensed' (darkly stained) chromosomes of dinoflagellates decondense by swelling. This occurs in an increasing number of cells when the concentration of added OsO4 is decreased. With different fixatives other types of disintegration can be observed, which vary with the concentration. With cryofixation and freeze-substitution the chromosomes are most 'condensed'. Escherichia coli infected with bacteriophage T4, with or without active lysozyme production, were studied by optical densitometry for partial lysis and by light and electron microscopy for observing swelling. When active lysozyme is present some of the acrolein (2.5%)-glutaraldehyde (2%)-fixed cells swell at 0 degrees C, but do not in the absence of lysozyme nor when fixed at room temperature. If OsO4 is added at concentrations < or = 0.5%, partial lysis occurs when lysozyme is present. The optical density decreases, the cells lose some matter and swell slightly. The corresponding electron micrographs show gap formation by curdling and/or a decreased concentration of the cytoplasm which reveals certain phage-related particles.

Animals↗

PubMed1991

Storage, ultrastructural targeting and function of toposomes and hyalin in sea urchin embryogenesis.

This study compares by immunogold labeling the ultrastructural localization of a hexameric 22S glycoprotein, called toposome, with that of hyalin in unfertilized eggs and cells of hatched sea urchin blastulae. Nearly all hyalin is present in the electron translucent compartment of the cortical granules and in the translucent non-cortical pigment granules. In the blastula both of these intracellular stores have vanished and hyalin now forms a broad band below the apical lamina. By contrast, in the egg toposomes are present on the surface, as well as stored in yolk granules and in the electron dense lamellar compartment of the cortical granules. In the hatched blastula, toposomes that have been modified by limited proteolysis in the yolk granules, are associated with the plasma membranes of all newly formed cells, while the toposomes originating from the cortical granules have been incorporated as unmodified 160 kDa polypeptides into an extracellular double layer enveloping the embryo on the outside of the hyaline layer. From evidence discussed in detail, we conclude that the extracellular toposomes rivet the apical lamina to the surface and underlying cytoskeleton of the microvilli, while the modified toposomes from the yolk granules are responsible for position specific intercellular adhesion as they are released to the surface of newly formed cells. We propose that all the material stored in yolk granules is utilized for the assembly of new membranes.

Animals↗

PubMed1991

Physiological, morphological, and physicochemical characterization of a novel Escherichia coli bacteriophage, phage MM.

A double-stranded DNA containing, T even-like, Escherichia coli bacteriophage, called MM, has been isolated from the local sewage and purified by polyethylene glycol precipitation followed by banding on a cesium chloride three-step gradient. It yields a burst size of 75 particles per infected cell, and has an adsorption coefficient of 3.3 x 10(-10) cm3/min and a latent period of 45 min. Electron microscopy of phage MM reveals an isometric icosahedral head, 92 nm long and 81 nm wide, and a 112-nm-long contractile tail with six pairs of 40-nm-long fibers attached to its baseplate. Phage MM appears similar to E. coli phage T4 or Salmonella phage O1. The density of phage MM in cesium chloride is 1.515 g/ml, and its total mass is 144 MDa. Gel electrophoresis of purified MM capsids displays two major capsid proteins in approximately equimolar amounts and with apparent molecular masses of 38 and 15 kDa. Similarly, purified MM tails yield two major polypeptides with apparent molecular masses of 55 and 16 kDa, most likely representing the major tail sheath and tail tube polypeptides. Its double-stranded DNA has a G-C content of 50%, a length of 131 kilobases (kb), and a mass of 89 MDa.

Adsorption↗

PubMed1991

Mass analysis of bacteriophage T4 proheads and mature heads by scanning transmission electron microscopy and hydrodynamic measurements.

Quantitative mass analysis of bacteriophage T4 proheads by scanning transmission electron microscopy (STEM) revealed a mass of 79.5 +/- 0.6 MDa, while hydrodynamic measurements yielded a prohead mass of about 80 MDa. This is 25% less than the prohead mass deduced from its polypeptide composition, and this finding implies that the bacteriophage T4 prohead is built of fewer polypeptide copies than previously reported. In contrast, the mass of mature heads measured by STEM, 194 +/- 2 MDa, is in agreement with previous mass measurements of DNA and protein content, and it is consistent with the previously determined stoichiometry. This good agreement of average STEM values for proheads and mature heads with corresponding hydrodynamic measurements suggests that STEM allows faithful evaluation of the masses of large supramolecular assemblies (i.e., greater than or equal to 200 MDa) such as whole viruses or cellular organelles.

Formaldehyde↗

PubMed1991

The potential of cryofixation and freeze substitution: observations and theoretical considerations.

The theoretical and experimental evidence in favour of cryofixation and freeze-substitution are critically reviewed. The solubility of macromolecules in water is due to the hydration shells. Their behaviour at different temperatures and the consequences of their removal during the processing for embedding are explained. Gelation prior to the transfer into solvents prevents macromolecules aggregating. During substitution at low temperatures, DNA is gelled, justifying the use of the term cryofixation. It is proposed that the preservation of hydration shells at the lowest temperature, and their transformation into minute gaps after a rise of temperature, facilitates the exhibition of epitopes.

Animals↗