Using protein synthesis inhibitors to establish the phylogenetic relationships of the sulfolobales order

The sensitivity of the cell-free protein synthesis systems from Acidanus brierleyi, Acidianus infernus, and Metallosphaera sedula, members of the archaeal order Sulfolobales, to 40 antibiotics with different specificities has been studied. The sensitivity patterns were compared to those of Sulfolobus solfataricus and other archaeal, bacterial, and eukaryotic systems. The comparative analysis shows that ribosomes from the sulfolobales are the most refractory to inhibitors of protein synthesis described so far. The sensitivity results have been used to ascertain in phylogenetic relationships among the members of the order Sulfolobales. The evolutionary significance of these results are analyzed in the context of the phylogenetic position of this group of extreme thermophilic microorganisms. Correspondence to: R. Amils     

Early helper T-cell dysfunction in simian immunodeficiency virus but not in human immunodeficiency virus type-2-infected macaques

Both naive and vaccinated macaques acquired a virus-specific proliferative helper T-cell reactivity in response to infection with the nonpathogenic human immunodeficiency virus type 2 (HIV-2). In contrast, macaques infected with the pathogenic simian immunodeficiency virus of the macaque strain (SIV_mac) did not develop a helper T-cell response. Furthermore, a vaccine-induced preexisting T-cell reactivity was abrogated after SIV_mac infection in vaccine failures. These differences may reflect the different pathogenicity of the two closely related viruses.     

Effects of amphipathic peptides,including presequences,on the functional integrity of rat liver mitochondrial membranes

A number of amphipathic peptides were tested for their effects on structural and functional properties of isolated rat liver mitochondria. The peptides included the matrix targeting sequence of subunit IV of (yeast) cytochromec oxidase. Titration experiments in which the mitochondria were incubated with increasing concentrations of the peptides revealed two major stages in the interaction. First, at low peptide/mitochondria ratios, peptide binding to the outer membrane occurred which was accompanied by gradual lysis of the outer membrane at higher ratios. The latter was deduced from the release of adenylate kinase, the classical marker enzyme of the intermembrane space. Secondly, at still higher peptide/mitochondria ratios, the permeability of the inner membrane progressively increased, as evidenced by measurements of respiratory control and of the membrane potential. Complete uncoupling of respiration seemed to precede dissipation of the membrane potential.     

Comparative structure of vesicular-arbuscular mycorrhizas and ectomycorrhizas

During the establishment of vesicular-arbuscular mycorrhizas, fungal hyphae contact the root surface, form appressoria and initiate the internal colonization phase. Structural changes occur in the cell wall, the cytoplasm and the nucleus as the fungus progresses from a presymbiotic to a symbiotic phase. Nuclei in spores are in G₁ whereas in intraradical hyphae they are in G₁ and G₂. Changes in nuclear organization are evident in various stages in the colonization process. Dramatic changes in both symbionts occur as the nutrient exchange interface is established between arbuscules and root cortical cells. An interfacial matrix, consisting of molecules common to the primary wall of the cortical cell, separates the cortical cell plasma membrane from the fungal cell wall. Ectomycorrhizas are characterized structurally by the presence of a mantle of fungal hyphae enclosing the root and usually an Hartig net of intercellular hyphae characterized by labyrinthine branching. As hyphae contact the root surface, they may respond by increasing their diameter and switching from apical growth to precocious branching. The site of initial contact of hyphae may be either the root cap or the ‘mycorrhiza infection zone’. The mantle varies considerably in structure depending on both the plant and fungus genome. In some ectomycorrhizas, the mantle may be a barrier to apoplastic transport, and in most it may store polyphosphate, glycogen, lipids and perhaps protein.     

The pharmacophore of the human C5a anaphylatoxin.

We have determined which amino acids contribute to the pharmacophore of human C5a, a potent inflammatory mediator. A systematic mutational analysis of this 74-amino acid protein was performed and the effects on the potency of receptor binding and of C5a-induced intracellular calcium ion mobilization were measured. This analysis included the construction of hybrids between C5a and the homologous but unreactive C3a protein and site-directed mutagenesis. Ten noncontiguous amino acids from the structurally well-defined 4-helix core domain (amino acids 1-63) and the C-terminal arginine-containing tripeptide were found to contribute to the pharmacophore of human C5a. The 10 mostly charged amino acids from the core domain generally made small incremental contributions toward binding affinity, some of which were independent. Substitutions of the C-terminal amino acid Arg 74 produced the largest single effect. We also found the connection between these 2 important regions to be unconstrained.     

Detection of gaps in sinusoids by frog auditory nerve fibers: importance in AM coding

Physiological studies were carried out in the frog (Rana pipiens pipiens) eighth nerve to determine: (i) whether the modulation rate or the silent gap was the salient feature that set the upper limit of time-locking to pulsed amplitude-modulated (PAM) stimuli, (ii) the gap detection capacity of individual eighth nerve fibers. Time-locked responses of 79 eighth nerve fibers to PAM stimuli (at the fiber's characteristic frequency) showed that the synchronization coefficient was a low-pass function of the modulation rate. In response to PAM stimuli having different pulse durations, a fiber gave rise to non-overlapping modulation transfer functions. The upper cut-off frequency of time locking was higher when tonepulses in PAM stimuli had shorter duration. The fact that the cut-off frequency was different for the different PAM series suggested that the AM rate was neither the sole, nor the main, determinant for the decay in time-locking at high AM rates. Gap detection capacity was determined for 69 eighth nerve fibers by assessing fiber's spiking activities to paired tone-pulses during an OFF-window and an ON-window. It was found that the minimum detectable gap of eighth nerve fibers ranged from 0.5 to 10 ms with an average of 1.23–2.16 ms depending on the duration of paired tone pulses. For each fiber, the minimum detectable gap was longer when the duration of tone pulses comprising the twin-pulse stimuli was more than four times longer. When the synchronization coefficient was plotted against the silent gap between tones pulses in the PAM stimuli, the gap response functions of a fiber as derived from multiple PAM series were equivalent to gap response functions deriving from twin-pulse series suggesting that it was the silent gap which primarily determined the upper limit of time-locking to PAM stimuli.Abbreviations MTF modulation transfer function - PAM pulse amplitude modulated - SAM sinusoidally amplitude modulated - SC synchronization coefficient - TW time window     

Distribution of zinc metallothionein I mRNA in rat brain using in situ hybridization

Metallothionein (MT) isoforms I and II were first identified and characterized in our laboratories in several regions of brain, in hippocampal neurons in primary culture, and in retinoblastoma and neuroblastoma cell lines. In this study, by having employed the MT-I cDNA as a probe, we sought to gain additional insight about the function of MT by discerning the regional distribution of its mRNA. Northern blot analyses of brain mRNA revealed that the administration of zinc enhanced dramatically MT-I mRNA (570 bp). The in situ hybridization study revealed that MT-I mRNA was located in several areas of brain, with the highest concentrations found in the cerebellum, hippocampus, and ventricles. The results of these studies are interpreted to suggest that zinc enhances the synthesis of MT mRNA and MT in turn may participate in zinc associated functions in neurons.Abbreviations MT-I Metallothionein I isoform - mRNA Messenger ribonucleic acid - ³⁵S dCTP ³⁵S Deoxycytidine triphosphate - ³²P dCTP ³²P Deoxycytidine triphosphate - icv Intracerebroventricularly - IP Intraperitoneally - PBS Paraformaldehyde phosphate buffered saline solution - Tris 2 amino-2-hydroxymethylpropane-1,3 diol - EDTA Ethylenediaminetetraacetic acid - cDNA Complimentary deoxyribonucleic acid - bp Base pair     

Collective motions in proteins investigated by X-ray diffuse scattering

We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 Å, as well as to changes of the functional form of the correlation function. (3) But only the “average” value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe. © 1994 John Wiley & Sons, Inc.